Starting phenix.real_space_refine on Mon Jun 23 23:47:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2q_15101/06_2025/8a2q_15101.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2q_15101/06_2025/8a2q_15101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a2q_15101/06_2025/8a2q_15101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2q_15101/06_2025/8a2q_15101.map" model { file = "/net/cci-nas-00/data/ceres_data/8a2q_15101/06_2025/8a2q_15101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2q_15101/06_2025/8a2q_15101.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 56 5.49 5 S 68 5.16 5 C 9418 2.51 5 N 2591 2.21 5 O 2895 1.98 5 H 12784 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27812 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1119, 12650 Classifications: {'peptide': 1119} Link IDs: {'PTRANS': 46, 'TRANS': 1072} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1939 Unresolved non-hydrogen angles: 2675 Unresolved non-hydrogen dihedrals: 1294 Unresolved non-hydrogen chiralities: 458 Planarities with less than four sites: {'GLN:plan1': 40, 'HIS:plan': 12, 'TYR:plan': 5, 'ASN:plan1': 25, 'TRP:plan': 2, 'ASP:plan': 50, 'PHE:plan': 18, 'GLU:plan': 59, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 1004 Chain: "B" Number of atoms: 14136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 14136 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 31, 'TRANS': 1052} Chain breaks: 14 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1181 Unresolved non-hydrogen angles: 1545 Unresolved non-hydrogen dihedrals: 847 Unresolved non-hydrogen chiralities: 186 Planarities with less than four sites: {'GLN:plan1': 35, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 14, 'ASP:plan': 36, 'PHE:plan': 5, 'GLU:plan': 45, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 660 Chain: "S" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 515 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DG:plan2': 7, ' DC:plan2': 7, ' DA:plan2': 6, ' DG:plan': 7, ' DC:plan': 7, ' DT:plan': 8, ' DA:plan': 6, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 317 Chain: "T" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 511 Classifications: {'DNA': 29} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 28} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 515 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DG:plan2': 7, ' DC:plan2': 7, ' DA:plan2': 7, ' DG:plan': 7, ' DC:plan': 7, ' DT%3*END:plan': 1, ' DT:plan': 6, ' DA:plan': 7, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 320 Time building chain proxies: 13.44, per 1000 atoms: 0.48 Number of scatterers: 27812 At special positions: 0 Unit cell: (129, 171.14, 116.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 56 15.00 O 2895 8.00 N 2591 7.00 C 9418 6.00 H 12784 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.63 Conformation dependent library (CDL) restraints added in 2.7 seconds 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 3 sheets defined 81.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.94 Creating SS restraints... Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.834A pdb=" N SER A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 removed outlier: 3.893A pdb=" N PHE A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN A 78 " --> pdb=" O GLN A 74 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 Proline residue: A 92 - end of helix No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 93 through 108 removed outlier: 4.140A pdb=" N GLU A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 148 through 163 removed outlier: 3.598A pdb=" N VAL A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 175 through 184 removed outlier: 4.051A pdb=" N ILE A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 206 removed outlier: 3.703A pdb=" N VAL A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 222 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.646A pdb=" N GLN A 240 " --> pdb=" O CYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 255 Processing helix chain 'A' and resid 258 through 272 removed outlier: 3.951A pdb=" N ALA A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 removed outlier: 3.700A pdb=" N ASN A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.027A pdb=" N ASP A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 360 removed outlier: 3.684A pdb=" N LYS A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 374 removed outlier: 3.521A pdb=" N SER A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.818A pdb=" N LYS A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.798A pdb=" N ASN A 422 " --> pdb=" O GLN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.516A pdb=" N ILE A 431 " --> pdb=" O HIS A 427 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.981A pdb=" N LEU A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS A 447 " --> pdb=" O GLN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.796A pdb=" N ALA A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 486 removed outlier: 3.798A pdb=" N SER A 486 " --> pdb=" O THR A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 506 Processing helix chain 'A' and resid 506 through 513 removed outlier: 4.013A pdb=" N LEU A 510 " --> pdb=" O HIS A 506 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.665A pdb=" N VAL A 517 " --> pdb=" O TYR A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 546 Processing helix chain 'A' and resid 550 through 566 removed outlier: 3.753A pdb=" N ASP A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.736A pdb=" N ILE A 577 " --> pdb=" O LYS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 removed outlier: 4.019A pdb=" N LEU A 612 " --> pdb=" O CYS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 644 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 658 through 668 removed outlier: 4.516A pdb=" N GLU A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) Proline residue: A 665 - end of helix Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 731 through 747 Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 756 through 758 No H-bonds generated for 'chain 'A' and resid 756 through 758' Processing helix chain 'A' and resid 766 through 771 Processing helix chain 'A' and resid 772 through 776 Processing helix chain 'A' and resid 780 through 803 Processing helix chain 'A' and resid 809 through 834 removed outlier: 3.558A pdb=" N LYS A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 830 " --> pdb=" O ASN A 826 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 936 removed outlier: 3.626A pdb=" N LEU A 935 " --> pdb=" O PHE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 979 removed outlier: 3.876A pdb=" N HIS A 977 " --> pdb=" O TRP A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1006 Processing helix chain 'A' and resid 1007 through 1018 removed outlier: 3.765A pdb=" N LEU A1018 " --> pdb=" O CYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1036 removed outlier: 3.668A pdb=" N LEU A1022 " --> pdb=" O LEU A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1072 Processing helix chain 'A' and resid 1073 through 1080 removed outlier: 5.323A pdb=" N HIS A1079 " --> pdb=" O PHE A1076 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A1080 " --> pdb=" O SER A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1097 Processing helix chain 'A' and resid 1105 through 1119 Processing helix chain 'A' and resid 1120 through 1123 Processing helix chain 'A' and resid 1126 through 1141 removed outlier: 3.580A pdb=" N ALA A1130 " --> pdb=" O SER A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1163 Processing helix chain 'A' and resid 1175 through 1193 removed outlier: 3.609A pdb=" N HIS A1192 " --> pdb=" O VAL A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1215 removed outlier: 4.602A pdb=" N VAL A1208 " --> pdb=" O SER A1204 " (cutoff:3.500A) Proline residue: A1209 - end of helix removed outlier: 3.605A pdb=" N SER A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1248 removed outlier: 3.541A pdb=" N PHE A1234 " --> pdb=" O THR A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1281 removed outlier: 4.009A pdb=" N GLU A1263 " --> pdb=" O GLU A1259 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A1281 " --> pdb=" O ILE A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1284 No H-bonds generated for 'chain 'A' and resid 1282 through 1284' Processing helix chain 'A' and resid 1287 through 1316 removed outlier: 4.022A pdb=" N ARG A1299 " --> pdb=" O LEU A1295 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A1300 " --> pdb=" O LYS A1296 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET A1310 " --> pdb=" O LEU A1306 " (cutoff:3.500A) Proline residue: A1311 - end of helix Processing helix chain 'A' and resid 1321 through 1349 removed outlier: 3.854A pdb=" N LEU A1333 " --> pdb=" O LYS A1329 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A1334 " --> pdb=" O THR A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1355 removed outlier: 4.025A pdb=" N ASN A1355 " --> pdb=" O LEU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1377 removed outlier: 3.600A pdb=" N LEU A1360 " --> pdb=" O HIS A1356 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL A1368 " --> pdb=" O LEU A1364 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR A1369 " --> pdb=" O GLU A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1379 No H-bonds generated for 'chain 'A' and resid 1378 through 1379' Processing helix chain 'A' and resid 1380 through 1382 No H-bonds generated for 'chain 'A' and resid 1380 through 1382' Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 42 through 54 Processing helix chain 'B' and resid 61 through 79 removed outlier: 3.509A pdb=" N GLY B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 97 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 123 through 137 removed outlier: 4.265A pdb=" N LEU B 127 " --> pdb=" O ASN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 167 Processing helix chain 'B' and resid 173 through 184 Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.528A pdb=" N GLN B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 224 Processing helix chain 'B' and resid 225 through 245 removed outlier: 4.036A pdb=" N VAL B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 284 Processing helix chain 'B' and resid 285 through 302 removed outlier: 4.313A pdb=" N GLU B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.627A pdb=" N ALA B 348 " --> pdb=" O GLN B 344 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 356 removed outlier: 3.550A pdb=" N GLN B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 4.144A pdb=" N VAL B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 378 through 396 removed outlier: 3.902A pdb=" N MET B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 438 through 451 Processing helix chain 'B' and resid 458 through 472 removed outlier: 3.761A pdb=" N SER B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.640A pdb=" N ASN B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 479 " --> pdb=" O VAL B 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 474 through 479' Processing helix chain 'B' and resid 482 through 488 Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.111A pdb=" N GLY B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) Proline residue: B 507 - end of helix removed outlier: 3.626A pdb=" N VAL B 511 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 528 removed outlier: 3.754A pdb=" N ARG B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 528 " --> pdb=" O GLN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 549 removed outlier: 3.831A pdb=" N ALA B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 595 Processing helix chain 'B' and resid 596 through 598 No H-bonds generated for 'chain 'B' and resid 596 through 598' Processing helix chain 'B' and resid 600 through 618 removed outlier: 4.035A pdb=" N TYR B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY B 610 " --> pdb=" O MET B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 638 removed outlier: 3.595A pdb=" N SER B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR B 636 " --> pdb=" O GLN B 632 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 653 Processing helix chain 'B' and resid 665 through 684 Processing helix chain 'B' and resid 702 through 719 Processing helix chain 'B' and resid 737 through 765 removed outlier: 3.517A pdb=" N ILE B 745 " --> pdb=" O VAL B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 789 removed outlier: 3.868A pdb=" N ILE B 788 " --> pdb=" O LYS B 784 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 822 Processing helix chain 'B' and resid 831 through 839 removed outlier: 3.562A pdb=" N VAL B 835 " --> pdb=" O GLU B 831 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 836 " --> pdb=" O SER B 832 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER B 839 " --> pdb=" O VAL B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 860 removed outlier: 3.569A pdb=" N MET B 843 " --> pdb=" O SER B 839 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 850 " --> pdb=" O ALA B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 892 removed outlier: 3.699A pdb=" N ARG B 883 " --> pdb=" O CYS B 879 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 884 " --> pdb=" O LYS B 880 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 892 " --> pdb=" O ARG B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 925 Processing helix chain 'B' and resid 929 through 937 removed outlier: 3.569A pdb=" N PHE B 933 " --> pdb=" O ARG B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 972 removed outlier: 3.792A pdb=" N LYS B 954 " --> pdb=" O ASN B 950 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG B 964 " --> pdb=" O ARG B 960 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER B 965 " --> pdb=" O GLN B 961 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 966 " --> pdb=" O PHE B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 994 removed outlier: 4.144A pdb=" N LYS B 994 " --> pdb=" O SER B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1017 removed outlier: 3.814A pdb=" N LEU B1004 " --> pdb=" O SER B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1038 removed outlier: 4.156A pdb=" N LEU B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1057 Processing helix chain 'B' and resid 1081 through 1107 removed outlier: 3.693A pdb=" N CYS B1085 " --> pdb=" O ALA B1081 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN B1091 " --> pdb=" O LEU B1087 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B1104 " --> pdb=" O ASP B1100 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B1105 " --> pdb=" O TRP B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1147 removed outlier: 3.682A pdb=" N LEU B1133 " --> pdb=" O LYS B1129 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN B1134 " --> pdb=" O GLY B1130 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B1135 " --> pdb=" O VAL B1131 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR B1140 " --> pdb=" O GLY B1136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B1141 " --> pdb=" O THR B1137 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN B1147 " --> pdb=" O HIS B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1153 through 1180 removed outlier: 3.966A pdb=" N ASP B1157 " --> pdb=" O GLY B1153 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS B1176 " --> pdb=" O SER B1172 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B1177 " --> pdb=" O LEU B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1189 through 1203 Processing helix chain 'B' and resid 1203 through 1225 removed outlier: 4.117A pdb=" N TYR B1208 " --> pdb=" O THR B1204 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B1209 " --> pdb=" O PRO B1205 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B1215 " --> pdb=" O ILE B1211 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN B1216 " --> pdb=" O THR B1212 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE B1224 " --> pdb=" O GLU B1220 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B1225 " --> pdb=" O SER B1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 1243 through 1251 Processing helix chain 'B' and resid 1253 through 1274 Processing helix chain 'B' and resid 1278 through 1282 removed outlier: 3.599A pdb=" N TYR B1282 " --> pdb=" O LEU B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1295 through 1299 removed outlier: 3.859A pdb=" N ASP B1299 " --> pdb=" O SER B1296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 669 through 670 Processing sheet with id=AA2, first strand: chain 'A' and resid 685 through 687 Processing sheet with id=AA3, first strand: chain 'A' and resid 1384 through 1389 removed outlier: 3.611A pdb=" N TRP A1385 " --> pdb=" O ARG B1292 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A1387 " --> pdb=" O ASP B1290 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER B1288 " --> pdb=" O LEU A1389 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.90 Time building geometry restraints manager: 9.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 12743 1.03 - 1.23: 46 1.23 - 1.42: 6089 1.42 - 1.62: 9129 1.62 - 1.81: 96 Bond restraints: 28103 Sorted by residual: bond pdb=" C SER A 786 " pdb=" O SER A 786 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.15e-02 7.56e+03 2.82e+01 bond pdb=" C ASP B 361 " pdb=" N VAL B 362 " ideal model delta sigma weight residual 1.333 1.273 0.060 1.24e-02 6.50e+03 2.36e+01 bond pdb=" N ASP B 361 " pdb=" H ASP B 361 " ideal model delta sigma weight residual 0.860 0.917 -0.057 2.00e-02 2.50e+03 8.11e+00 bond pdb=" C TYR B 360 " pdb=" N ASP B 361 " ideal model delta sigma weight residual 1.331 1.290 0.040 1.42e-02 4.96e+03 8.05e+00 bond pdb=" N SER A 786 " pdb=" H SER A 786 " ideal model delta sigma weight residual 0.860 0.916 -0.056 2.00e-02 2.50e+03 7.92e+00 ... (remaining 28098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 49126 2.45 - 4.91: 651 4.91 - 7.36: 66 7.36 - 9.82: 5 9.82 - 12.27: 4 Bond angle restraints: 49852 Sorted by residual: angle pdb=" C3' DG S 27 " pdb=" O3' DG S 27 " pdb=" P DA S 28 " ideal model delta sigma weight residual 120.20 130.76 -10.56 1.50e+00 4.44e-01 4.95e+01 angle pdb=" CA SER A 786 " pdb=" C SER A 786 " pdb=" O SER A 786 " ideal model delta sigma weight residual 120.82 114.85 5.97 1.05e+00 9.07e-01 3.24e+01 angle pdb=" C4' DG S 27 " pdb=" C3' DG S 27 " pdb=" O3' DG S 27 " ideal model delta sigma weight residual 110.00 101.86 8.14 1.50e+00 4.44e-01 2.94e+01 angle pdb=" O3' DG S 18 " pdb=" C3' DG S 18 " pdb=" C2' DG S 18 " ideal model delta sigma weight residual 111.50 119.19 -7.69 1.50e+00 4.44e-01 2.63e+01 angle pdb=" CA LEU A1063 " pdb=" C LEU A1063 " pdb=" O LEU A1063 " ideal model delta sigma weight residual 120.70 115.73 4.97 1.03e+00 9.43e-01 2.32e+01 ... (remaining 49847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.10: 12779 33.10 - 66.21: 578 66.21 - 99.31: 30 99.31 - 132.41: 1 132.41 - 165.51: 1 Dihedral angle restraints: 13389 sinusoidal: 7059 harmonic: 6330 Sorted by residual: dihedral pdb=" CA PHE A 435 " pdb=" C PHE A 435 " pdb=" N PRO A 436 " pdb=" CA PRO A 436 " ideal model delta harmonic sigma weight residual -180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" C4' DC S 19 " pdb=" C3' DC S 19 " pdb=" O3' DC S 19 " pdb=" P DT S 20 " ideal model delta sinusoidal sigma weight residual 220.00 54.49 165.51 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DT S 8 " pdb=" C3' DT S 8 " pdb=" O3' DT S 8 " pdb=" P DC S 9 " ideal model delta sinusoidal sigma weight residual -140.00 -14.70 -125.30 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 13386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2011 0.057 - 0.114: 326 0.114 - 0.171: 28 0.171 - 0.228: 2 0.228 - 0.286: 2 Chirality restraints: 2369 Sorted by residual: chirality pdb=" C3' DG S 27 " pdb=" C4' DG S 27 " pdb=" O3' DG S 27 " pdb=" C2' DG S 27 " both_signs ideal model delta sigma weight residual False -2.66 -2.95 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C3' DC S 9 " pdb=" C4' DC S 9 " pdb=" O3' DC S 9 " pdb=" C2' DC S 9 " both_signs ideal model delta sigma weight residual False -2.66 -2.41 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C3' DC S 19 " pdb=" C4' DC S 19 " pdb=" O3' DC S 19 " pdb=" C2' DC S 19 " both_signs ideal model delta sigma weight residual False -2.66 -2.45 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2366 not shown) Planarity restraints: 4717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 638 " 0.062 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 639 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 639 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 639 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 210 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.79e+00 pdb=" N PRO B 211 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 211 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 211 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 664 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO B 665 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " -0.035 5.00e-02 4.00e+02 ... (remaining 4714 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 3705 2.29 - 2.87: 56422 2.87 - 3.45: 66040 3.45 - 4.02: 79288 4.02 - 4.60: 122899 Nonbonded interactions: 328354 Sorted by model distance: nonbonded pdb=" O GLY B 777 " pdb=" HG1 THR B 780 " model vdw 1.718 2.450 nonbonded pdb=" O LEU A 758 " pdb="HH21 ARG A 817 " model vdw 1.730 2.450 nonbonded pdb=" OE2 GLU A1210 " pdb=" H THR A1222 " model vdw 1.738 2.450 nonbonded pdb=" HD1 HIS A1030 " pdb=" OG SER A1123 " model vdw 1.753 2.450 nonbonded pdb=" O ASN B1278 " pdb="HE21 GLN B1281 " model vdw 1.756 2.450 ... (remaining 328349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.550 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 67.210 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 15319 Z= 0.222 Angle : 0.792 10.559 20774 Z= 0.450 Chirality : 0.041 0.286 2369 Planarity : 0.005 0.091 2618 Dihedral : 16.573 165.515 5306 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.75 % Rotamer: Outliers : 0.17 % Allowed : 0.41 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.18), residues: 2151 helix: 2.08 (0.13), residues: 1580 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 679 HIS 0.011 0.001 HIS B 276 PHE 0.019 0.001 PHE B 611 TYR 0.038 0.001 TYR A 633 ARG 0.006 0.000 ARG B 616 Details of bonding type rmsd hydrogen bonds : bond 0.14317 ( 1178) hydrogen bonds : angle 4.80782 ( 3465) covalent geometry : bond 0.00459 (15319) covalent geometry : angle 0.79231 (20774) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue TYR 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue ILE 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 200 is missing expected H atoms. Skipping. Residue MET 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 239 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue VAL 246 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue MET 270 is missing expected H atoms. Skipping. Residue ILE 272 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue ALA 297 is missing expected H atoms. Skipping. Residue ILE 301 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 400 is missing expected H atoms. Skipping. Residue THR 402 is missing expected H atoms. Skipping. Residue LYS 404 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue MET 420 is missing expected H atoms. Skipping. Residue SER 428 is missing expected H atoms. Skipping. Residue MET 429 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue ALA 464 is missing expected H atoms. Skipping. Residue ALA 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue TYR 471 is missing expected H atoms. Skipping. Residue VAL 476 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue ILE 504 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue SER 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue TYR 513 is missing expected H atoms. Skipping. Residue ALA 514 is missing expected H atoms. Skipping. Residue THR 515 is missing expected H atoms. Skipping. Residue VAL 517 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue THR 519 is missing expected H atoms. Skipping. Residue ILE 520 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue SER 523 is missing expected H atoms. Skipping. Residue MET 524 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LYS 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue SER 540 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue SER 545 is missing expected H atoms. Skipping. Residue SER 551 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue MET 559 is missing expected H atoms. Skipping. Residue LYS 563 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue SER 567 is missing expected H atoms. Skipping. Residue SER 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue MET 575 is missing expected H atoms. Skipping. Residue THR 582 is missing expected H atoms. Skipping. Residue MET 583 is missing expected H atoms. Skipping. Residue SER 586 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue SER 613 is missing expected H atoms. Skipping. Residue THR 614 is missing expected H atoms. Skipping. Residue LEU 615 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue THR 626 is missing expected H atoms. Skipping. Residue ALA 638 is missing expected H atoms. Skipping. Residue LYS 643 is missing expected H atoms. Skipping. Residue LYS 645 is missing expected H atoms. Skipping. Residue LEU 648 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LEU 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue VAL 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 672 is missing expected H atoms. Skipping. Residue SER 673 is missing expected H atoms. Skipping. Residue THR 675 is missing expected H atoms. Skipping. Residue VAL 676 is missing expected H atoms. Skipping. Residue SER 679 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 690 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue ALA 698 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue VAL 727 is missing expected H atoms. Skipping. Residue SER 728 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue ILE 754 is missing expected H atoms. Skipping. Residue LEU 764 is missing expected H atoms. Skipping. Residue THR 765 is missing expected H atoms. Skipping. Residue LEU 767 is missing expected H atoms. Skipping. Residue VAL 769 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 775 is missing expected H atoms. Skipping. Residue LEU 776 is missing expected H atoms. Skipping. Residue SER 777 is missing expected H atoms. Skipping. Residue ALA 791 is missing expected H atoms. Skipping. Residue ALA 808 is missing expected H atoms. Skipping. Residue MET 810 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ALA 833 is missing expected H atoms. Skipping. Residue ALA 834 is missing expected H atoms. Skipping. Residue THR 835 is missing expected H atoms. Skipping. Residue VAL 839 is missing expected H atoms. Skipping. Residue ALA 843 is missing expected H atoms. Skipping. Residue LEU 917 is missing expected H atoms. Skipping. Residue SER 919 is missing expected H atoms. Skipping. Residue TYR 920 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue ALA 962 is missing expected H atoms. Skipping. Residue THR 980 is missing expected H atoms. Skipping. Residue LYS 1009 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1020 is missing expected H atoms. Skipping. Residue THR 1035 is missing expected H atoms. Skipping. Residue VAL 1036 is missing expected H atoms. Skipping. Residue ILE 1050 is missing expected H atoms. Skipping. Residue SER 1082 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue THR 1101 is missing expected H atoms. Skipping. Residue LEU 1104 is missing expected H atoms. Skipping. Residue SER 1141 is missing expected H atoms. Skipping. Residue LYS 1143 is missing expected H atoms. Skipping. Residue MET 1166 is missing expected H atoms. Skipping. Residue LYS 1174 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue ALA 1199 is missing expected H atoms. Skipping. Residue LYS 1216 is missing expected H atoms. Skipping. Residue SER 1227 is missing expected H atoms. Skipping. Residue LYS 1253 is missing expected H atoms. Skipping. Residue SER 1257 is missing expected H atoms. Skipping. Residue SER 1287 is missing expected H atoms. Skipping. Residue LYS 1307 is missing expected H atoms. Skipping. Residue LYS 1318 is missing expected H atoms. Skipping. Residue LYS 1319 is missing expected H atoms. Skipping. Residue LYS 1329 is missing expected H atoms. Skipping. Residue ALA 1373 is missing expected H atoms. Skipping. Residue LYS 1390 is missing expected H atoms. Skipping. Residue MET 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue TYR 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue THR 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue THR 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue VAL 380 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue TYR 395 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue VAL 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue ALA 454 is missing expected H atoms. Skipping. Residue ALA 455 is missing expected H atoms. Skipping. Residue SER 456 is missing expected H atoms. Skipping. Residue ALA 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue SER 479 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue ALA 504 is missing expected H atoms. Skipping. Residue SER 512 is missing expected H atoms. Skipping. Residue MET 513 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue ALA 526 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 534 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue LEU 552 is missing expected H atoms. Skipping. Residue ALA 584 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue SER 598 is missing expected H atoms. Skipping. Residue ALA 601 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue MET 626 is missing expected H atoms. Skipping. Residue LYS 634 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue LEU 643 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue LEU 647 is missing expected H atoms. Skipping. Residue LYS 648 is missing expected H atoms. Skipping. Residue LEU 649 is missing expected H atoms. Skipping. Residue ILE 653 is missing expected H atoms. Skipping. Residue MET 654 is missing expected H atoms. Skipping. Residue ILE 660 is missing expected H atoms. Skipping. Residue ALA 667 is missing expected H atoms. Skipping. Residue THR 683 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue MET 709 is missing expected H atoms. Skipping. Residue LYS 719 is missing expected H atoms. Skipping. Residue SER 720 is missing expected H atoms. Skipping. Residue LEU 722 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue VAL 739 is missing expected H atoms. Skipping. Residue LYS 742 is missing expected H atoms. Skipping. Residue LYS 763 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue SER 807 is missing expected H atoms. Skipping. Residue ALA 820 is missing expected H atoms. Skipping. Residue ALA 826 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LEU 833 is missing expected H atoms. Skipping. Residue LEU 836 is missing expected H atoms. Skipping. Residue SER 839 is missing expected H atoms. Skipping. Residue ALA 846 is missing expected H atoms. Skipping. Residue MET 860 is missing expected H atoms. Skipping. Residue LYS 873 is missing expected H atoms. Skipping. Residue SER 891 is missing expected H atoms. Skipping. Residue ILE 892 is missing expected H atoms. Skipping. Residue SER 906 is missing expected H atoms. Skipping. Residue ILE 949 is missing expected H atoms. Skipping. Residue SER 972 is missing expected H atoms. Skipping. Residue LEU 1019 is missing expected H atoms. Skipping. Residue LEU 1022 is missing expected H atoms. Skipping. Residue SER 1070 is missing expected H atoms. Skipping. Residue ILE 1074 is missing expected H atoms. Skipping. Residue LYS 1078 is missing expected H atoms. Skipping. Residue THR 1107 is missing expected H atoms. Skipping. Residue THR 1124 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Residue ALA 1180 is missing expected H atoms. Skipping. Residue VAL 1188 is missing expected H atoms. Skipping. Residue ILE 1217 is missing expected H atoms. Skipping. Residue SER 1219 is missing expected H atoms. Skipping. Residue SER 1221 is missing expected H atoms. Skipping. Residue SER 1223 is missing expected H atoms. Skipping. Residue LYS 1274 is missing expected H atoms. Skipping. Residue SER 1275 is missing expected H atoms. Skipping. Residue MET 1297 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 84 average time/residue: 0.3835 time to fit residues: 56.2735 Evaluate side-chains 68 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 188 optimal weight: 7.9990 chunk 169 optimal weight: 30.0000 chunk 93 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 114 optimal weight: 30.0000 chunk 90 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 852 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.085414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.058439 restraints weight = 184902.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.060359 restraints weight = 69317.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.061478 restraints weight = 37834.573| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15319 Z= 0.130 Angle : 0.484 5.551 20774 Z= 0.270 Chirality : 0.034 0.128 2369 Planarity : 0.004 0.062 2618 Dihedral : 16.269 171.153 2834 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 0.25 % Allowed : 2.89 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.19), residues: 2151 helix: 2.71 (0.13), residues: 1610 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 679 HIS 0.006 0.001 HIS A1061 PHE 0.011 0.001 PHE A 966 TYR 0.010 0.001 TYR B 746 ARG 0.002 0.000 ARG B 616 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 1178) hydrogen bonds : angle 3.90807 ( 3465) covalent geometry : bond 0.00268 (15319) covalent geometry : angle 0.48425 (20774) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue TYR 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue ILE 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 200 is missing expected H atoms. Skipping. Residue MET 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 239 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue VAL 246 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue MET 270 is missing expected H atoms. Skipping. Residue ILE 272 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue ALA 297 is missing expected H atoms. Skipping. Residue ILE 301 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 400 is missing expected H atoms. Skipping. Residue THR 402 is missing expected H atoms. Skipping. Residue LYS 404 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue MET 420 is missing expected H atoms. Skipping. Residue SER 428 is missing expected H atoms. Skipping. Residue MET 429 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue ALA 464 is missing expected H atoms. Skipping. Residue ALA 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue TYR 471 is missing expected H atoms. Skipping. Residue VAL 476 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue ILE 504 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue SER 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue TYR 513 is missing expected H atoms. Skipping. Residue ALA 514 is missing expected H atoms. Skipping. Residue THR 515 is missing expected H atoms. Skipping. Residue VAL 517 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue THR 519 is missing expected H atoms. Skipping. Residue ILE 520 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue SER 523 is missing expected H atoms. Skipping. Residue MET 524 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LYS 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue SER 540 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue SER 545 is missing expected H atoms. Skipping. Residue SER 551 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue MET 559 is missing expected H atoms. Skipping. Residue LYS 563 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue SER 567 is missing expected H atoms. Skipping. Residue SER 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue MET 575 is missing expected H atoms. Skipping. Residue THR 582 is missing expected H atoms. Skipping. Residue MET 583 is missing expected H atoms. Skipping. Residue SER 586 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue SER 613 is missing expected H atoms. Skipping. Residue THR 614 is missing expected H atoms. Skipping. Residue LEU 615 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue THR 626 is missing expected H atoms. Skipping. Residue ALA 638 is missing expected H atoms. Skipping. Residue LYS 643 is missing expected H atoms. Skipping. Residue LYS 645 is missing expected H atoms. Skipping. Residue LEU 648 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LEU 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue VAL 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 672 is missing expected H atoms. Skipping. Residue SER 673 is missing expected H atoms. Skipping. Residue THR 675 is missing expected H atoms. Skipping. Residue VAL 676 is missing expected H atoms. Skipping. Residue SER 679 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 690 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue ALA 698 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue VAL 727 is missing expected H atoms. Skipping. Residue SER 728 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue ILE 754 is missing expected H atoms. Skipping. Residue LEU 764 is missing expected H atoms. Skipping. Residue THR 765 is missing expected H atoms. Skipping. Residue LEU 767 is missing expected H atoms. Skipping. Residue VAL 769 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 775 is missing expected H atoms. Skipping. Residue LEU 776 is missing expected H atoms. Skipping. Residue SER 777 is missing expected H atoms. Skipping. Residue ALA 791 is missing expected H atoms. Skipping. Residue ALA 808 is missing expected H atoms. Skipping. Residue MET 810 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ALA 833 is missing expected H atoms. Skipping. Residue ALA 834 is missing expected H atoms. Skipping. Residue THR 835 is missing expected H atoms. Skipping. Residue VAL 839 is missing expected H atoms. Skipping. Residue ALA 843 is missing expected H atoms. Skipping. Residue LEU 917 is missing expected H atoms. Skipping. Residue SER 919 is missing expected H atoms. Skipping. Residue TYR 920 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue ALA 962 is missing expected H atoms. Skipping. Residue THR 980 is missing expected H atoms. Skipping. Residue LYS 1009 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1020 is missing expected H atoms. Skipping. Residue THR 1035 is missing expected H atoms. Skipping. Residue VAL 1036 is missing expected H atoms. Skipping. Residue ILE 1050 is missing expected H atoms. Skipping. Residue SER 1082 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue THR 1101 is missing expected H atoms. Skipping. Residue LEU 1104 is missing expected H atoms. Skipping. Residue SER 1141 is missing expected H atoms. Skipping. Residue LYS 1143 is missing expected H atoms. Skipping. Residue MET 1166 is missing expected H atoms. Skipping. Residue LYS 1174 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue ALA 1199 is missing expected H atoms. Skipping. Residue LYS 1216 is missing expected H atoms. Skipping. Residue SER 1227 is missing expected H atoms. Skipping. Residue LYS 1253 is missing expected H atoms. Skipping. Residue SER 1257 is missing expected H atoms. Skipping. Residue SER 1287 is missing expected H atoms. Skipping. Residue LYS 1307 is missing expected H atoms. Skipping. Residue LYS 1318 is missing expected H atoms. Skipping. Residue LYS 1319 is missing expected H atoms. Skipping. Residue LYS 1329 is missing expected H atoms. Skipping. Residue ALA 1373 is missing expected H atoms. Skipping. Residue LYS 1390 is missing expected H atoms. Skipping. Residue MET 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue TYR 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue THR 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue THR 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue VAL 380 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue TYR 395 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue VAL 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue ALA 454 is missing expected H atoms. Skipping. Residue ALA 455 is missing expected H atoms. Skipping. Residue SER 456 is missing expected H atoms. Skipping. Residue ALA 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue SER 479 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue ALA 504 is missing expected H atoms. Skipping. Residue SER 512 is missing expected H atoms. Skipping. Residue MET 513 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue ALA 526 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 534 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue LEU 552 is missing expected H atoms. Skipping. Residue ALA 584 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue SER 598 is missing expected H atoms. Skipping. Residue ALA 601 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue MET 626 is missing expected H atoms. Skipping. Residue LYS 634 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue LEU 643 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue LEU 647 is missing expected H atoms. Skipping. Residue LYS 648 is missing expected H atoms. Skipping. Residue LEU 649 is missing expected H atoms. Skipping. Residue ILE 653 is missing expected H atoms. Skipping. Residue MET 654 is missing expected H atoms. Skipping. Residue ILE 660 is missing expected H atoms. Skipping. Residue ALA 667 is missing expected H atoms. Skipping. Residue THR 683 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue MET 709 is missing expected H atoms. Skipping. Residue LYS 719 is missing expected H atoms. Skipping. Residue SER 720 is missing expected H atoms. Skipping. Residue LEU 722 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue VAL 739 is missing expected H atoms. Skipping. Residue LYS 742 is missing expected H atoms. Skipping. Residue LYS 763 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue SER 807 is missing expected H atoms. Skipping. Residue ALA 820 is missing expected H atoms. Skipping. Residue ALA 826 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LEU 833 is missing expected H atoms. Skipping. Residue LEU 836 is missing expected H atoms. Skipping. Residue SER 839 is missing expected H atoms. Skipping. Residue ALA 846 is missing expected H atoms. Skipping. Residue MET 860 is missing expected H atoms. Skipping. Residue LYS 873 is missing expected H atoms. Skipping. Residue SER 891 is missing expected H atoms. Skipping. Residue ILE 892 is missing expected H atoms. Skipping. Residue SER 906 is missing expected H atoms. Skipping. Residue ILE 949 is missing expected H atoms. Skipping. Residue SER 972 is missing expected H atoms. Skipping. Residue LEU 1019 is missing expected H atoms. Skipping. Residue LEU 1022 is missing expected H atoms. Skipping. Residue SER 1070 is missing expected H atoms. Skipping. Residue ILE 1074 is missing expected H atoms. Skipping. Residue LYS 1078 is missing expected H atoms. Skipping. Residue THR 1107 is missing expected H atoms. Skipping. Residue THR 1124 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Residue ALA 1180 is missing expected H atoms. Skipping. Residue VAL 1188 is missing expected H atoms. Skipping. Residue ILE 1217 is missing expected H atoms. Skipping. Residue SER 1219 is missing expected H atoms. Skipping. Residue SER 1221 is missing expected H atoms. Skipping. Residue SER 1223 is missing expected H atoms. Skipping. Residue LYS 1274 is missing expected H atoms. Skipping. Residue SER 1275 is missing expected H atoms. Skipping. Residue MET 1297 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 70 average time/residue: 0.3905 time to fit residues: 48.4471 Evaluate side-chains 67 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1171 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 5 optimal weight: 50.0000 chunk 147 optimal weight: 30.0000 chunk 168 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.083176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.056179 restraints weight = 187047.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.057965 restraints weight = 72053.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.059031 restraints weight = 40063.620| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15319 Z= 0.251 Angle : 0.558 7.112 20774 Z= 0.319 Chirality : 0.037 0.144 2369 Planarity : 0.004 0.058 2618 Dihedral : 15.534 170.195 2834 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 0.50 % Allowed : 5.29 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.18), residues: 2151 helix: 2.59 (0.13), residues: 1606 sheet: None (None), residues: 0 loop : -1.34 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1385 HIS 0.005 0.001 HIS A1025 PHE 0.018 0.002 PHE A 736 TYR 0.013 0.002 TYR A1297 ARG 0.005 0.000 ARG B 917 Details of bonding type rmsd hydrogen bonds : bond 0.05053 ( 1178) hydrogen bonds : angle 4.23188 ( 3465) covalent geometry : bond 0.00539 (15319) covalent geometry : angle 0.55783 (20774) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue TYR 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue ILE 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 200 is missing expected H atoms. Skipping. Residue MET 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 239 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue VAL 246 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue MET 270 is missing expected H atoms. Skipping. Residue ILE 272 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue ALA 297 is missing expected H atoms. Skipping. Residue ILE 301 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 400 is missing expected H atoms. Skipping. Residue THR 402 is missing expected H atoms. Skipping. Residue LYS 404 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue MET 420 is missing expected H atoms. Skipping. Residue SER 428 is missing expected H atoms. Skipping. Residue MET 429 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue ALA 464 is missing expected H atoms. Skipping. Residue ALA 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue TYR 471 is missing expected H atoms. Skipping. Residue VAL 476 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue ILE 504 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue SER 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue TYR 513 is missing expected H atoms. Skipping. Residue ALA 514 is missing expected H atoms. Skipping. Residue THR 515 is missing expected H atoms. Skipping. Residue VAL 517 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue THR 519 is missing expected H atoms. Skipping. Residue ILE 520 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue SER 523 is missing expected H atoms. Skipping. Residue MET 524 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LYS 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue SER 540 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue SER 545 is missing expected H atoms. Skipping. Residue SER 551 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue MET 559 is missing expected H atoms. Skipping. Residue LYS 563 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue SER 567 is missing expected H atoms. Skipping. Residue SER 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue MET 575 is missing expected H atoms. Skipping. Residue THR 582 is missing expected H atoms. Skipping. Residue MET 583 is missing expected H atoms. Skipping. Residue SER 586 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue SER 613 is missing expected H atoms. Skipping. Residue THR 614 is missing expected H atoms. Skipping. Residue LEU 615 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue THR 626 is missing expected H atoms. Skipping. Residue ALA 638 is missing expected H atoms. Skipping. Residue LYS 643 is missing expected H atoms. Skipping. Residue LYS 645 is missing expected H atoms. Skipping. Residue LEU 648 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LEU 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue VAL 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 672 is missing expected H atoms. Skipping. Residue SER 673 is missing expected H atoms. Skipping. Residue THR 675 is missing expected H atoms. Skipping. Residue VAL 676 is missing expected H atoms. Skipping. Residue SER 679 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 690 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue ALA 698 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue VAL 727 is missing expected H atoms. Skipping. Residue SER 728 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue ILE 754 is missing expected H atoms. Skipping. Residue LEU 764 is missing expected H atoms. Skipping. Residue THR 765 is missing expected H atoms. Skipping. Residue LEU 767 is missing expected H atoms. Skipping. Residue VAL 769 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 775 is missing expected H atoms. Skipping. Residue LEU 776 is missing expected H atoms. Skipping. Residue SER 777 is missing expected H atoms. Skipping. Residue ALA 791 is missing expected H atoms. Skipping. Residue ALA 808 is missing expected H atoms. Skipping. Residue MET 810 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ALA 833 is missing expected H atoms. Skipping. Residue ALA 834 is missing expected H atoms. Skipping. Residue THR 835 is missing expected H atoms. Skipping. Residue VAL 839 is missing expected H atoms. Skipping. Residue ALA 843 is missing expected H atoms. Skipping. Residue LEU 917 is missing expected H atoms. Skipping. Residue SER 919 is missing expected H atoms. Skipping. Residue TYR 920 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue ALA 962 is missing expected H atoms. Skipping. Residue THR 980 is missing expected H atoms. Skipping. Residue LYS 1009 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1020 is missing expected H atoms. Skipping. Residue THR 1035 is missing expected H atoms. Skipping. Residue VAL 1036 is missing expected H atoms. Skipping. Residue ILE 1050 is missing expected H atoms. Skipping. Residue SER 1082 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue THR 1101 is missing expected H atoms. Skipping. Residue LEU 1104 is missing expected H atoms. Skipping. Residue SER 1141 is missing expected H atoms. Skipping. Residue LYS 1143 is missing expected H atoms. Skipping. Residue MET 1166 is missing expected H atoms. Skipping. Residue LYS 1174 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue ALA 1199 is missing expected H atoms. Skipping. Residue LYS 1216 is missing expected H atoms. Skipping. Residue SER 1227 is missing expected H atoms. Skipping. Residue LYS 1253 is missing expected H atoms. Skipping. Residue SER 1257 is missing expected H atoms. Skipping. Residue SER 1287 is missing expected H atoms. Skipping. Residue LYS 1307 is missing expected H atoms. Skipping. Residue LYS 1318 is missing expected H atoms. Skipping. Residue LYS 1319 is missing expected H atoms. Skipping. Residue LYS 1329 is missing expected H atoms. Skipping. Residue ALA 1373 is missing expected H atoms. Skipping. Residue LYS 1390 is missing expected H atoms. Skipping. Residue MET 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue TYR 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue THR 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue THR 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue VAL 380 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue TYR 395 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue VAL 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue ALA 454 is missing expected H atoms. Skipping. Residue ALA 455 is missing expected H atoms. Skipping. Residue SER 456 is missing expected H atoms. Skipping. Residue ALA 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue SER 479 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue ALA 504 is missing expected H atoms. Skipping. Residue SER 512 is missing expected H atoms. Skipping. Residue MET 513 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue ALA 526 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 534 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue LEU 552 is missing expected H atoms. Skipping. Residue ALA 584 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue SER 598 is missing expected H atoms. Skipping. Residue ALA 601 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue MET 626 is missing expected H atoms. Skipping. Residue LYS 634 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue LEU 643 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue LEU 647 is missing expected H atoms. Skipping. Residue LYS 648 is missing expected H atoms. Skipping. Residue LEU 649 is missing expected H atoms. Skipping. Residue ILE 653 is missing expected H atoms. Skipping. Residue MET 654 is missing expected H atoms. Skipping. Residue ILE 660 is missing expected H atoms. Skipping. Residue ALA 667 is missing expected H atoms. Skipping. Residue THR 683 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue MET 709 is missing expected H atoms. Skipping. Residue LYS 719 is missing expected H atoms. Skipping. Residue SER 720 is missing expected H atoms. Skipping. Residue LEU 722 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue VAL 739 is missing expected H atoms. Skipping. Residue LYS 742 is missing expected H atoms. Skipping. Residue LYS 763 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue SER 807 is missing expected H atoms. Skipping. Residue ALA 820 is missing expected H atoms. Skipping. Residue ALA 826 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LEU 833 is missing expected H atoms. Skipping. Residue LEU 836 is missing expected H atoms. Skipping. Residue SER 839 is missing expected H atoms. Skipping. Residue ALA 846 is missing expected H atoms. Skipping. Residue MET 860 is missing expected H atoms. Skipping. Residue LYS 873 is missing expected H atoms. Skipping. Residue SER 891 is missing expected H atoms. Skipping. Residue ILE 892 is missing expected H atoms. Skipping. Residue SER 906 is missing expected H atoms. Skipping. Residue ILE 949 is missing expected H atoms. Skipping. Residue SER 972 is missing expected H atoms. Skipping. Residue LEU 1019 is missing expected H atoms. Skipping. Residue LEU 1022 is missing expected H atoms. Skipping. Residue SER 1070 is missing expected H atoms. Skipping. Residue ILE 1074 is missing expected H atoms. Skipping. Residue LYS 1078 is missing expected H atoms. Skipping. Residue THR 1107 is missing expected H atoms. Skipping. Residue THR 1124 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Residue ALA 1180 is missing expected H atoms. Skipping. Residue VAL 1188 is missing expected H atoms. Skipping. Residue ILE 1217 is missing expected H atoms. Skipping. Residue SER 1219 is missing expected H atoms. Skipping. Residue SER 1221 is missing expected H atoms. Skipping. Residue SER 1223 is missing expected H atoms. Skipping. Residue LYS 1274 is missing expected H atoms. Skipping. Residue SER 1275 is missing expected H atoms. Skipping. Residue MET 1297 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8480 (p0) cc_final: 0.8247 (p0) outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.3776 time to fit residues: 47.2953 Evaluate side-chains 68 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain B residue 1171 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 46 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 213 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 31 optimal weight: 0.0980 chunk 17 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.084209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.058705 restraints weight = 186465.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.060021 restraints weight = 78496.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.060147 restraints weight = 43460.342| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15319 Z= 0.141 Angle : 0.463 5.034 20774 Z= 0.261 Chirality : 0.034 0.126 2369 Planarity : 0.004 0.057 2618 Dihedral : 15.306 174.138 2834 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 0.17 % Allowed : 6.61 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.19), residues: 2151 helix: 2.92 (0.13), residues: 1615 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1385 HIS 0.003 0.001 HIS A1061 PHE 0.013 0.001 PHE A 966 TYR 0.011 0.001 TYR A1297 ARG 0.002 0.000 ARG B 616 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 1178) hydrogen bonds : angle 3.76190 ( 3465) covalent geometry : bond 0.00302 (15319) covalent geometry : angle 0.46339 (20774) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue TYR 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue ILE 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 200 is missing expected H atoms. Skipping. Residue MET 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 239 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue VAL 246 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue MET 270 is missing expected H atoms. Skipping. Residue ILE 272 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue ALA 297 is missing expected H atoms. Skipping. Residue ILE 301 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 400 is missing expected H atoms. Skipping. Residue THR 402 is missing expected H atoms. Skipping. Residue LYS 404 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue MET 420 is missing expected H atoms. Skipping. Residue SER 428 is missing expected H atoms. Skipping. Residue MET 429 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue ALA 464 is missing expected H atoms. Skipping. Residue ALA 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue TYR 471 is missing expected H atoms. Skipping. Residue VAL 476 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue ILE 504 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue SER 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue TYR 513 is missing expected H atoms. Skipping. Residue ALA 514 is missing expected H atoms. Skipping. Residue THR 515 is missing expected H atoms. Skipping. Residue VAL 517 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue THR 519 is missing expected H atoms. Skipping. Residue ILE 520 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue SER 523 is missing expected H atoms. Skipping. Residue MET 524 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LYS 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue SER 540 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue SER 545 is missing expected H atoms. Skipping. Residue SER 551 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue MET 559 is missing expected H atoms. Skipping. Residue LYS 563 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue SER 567 is missing expected H atoms. Skipping. Residue SER 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue MET 575 is missing expected H atoms. Skipping. Residue THR 582 is missing expected H atoms. Skipping. Residue MET 583 is missing expected H atoms. Skipping. Residue SER 586 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue SER 613 is missing expected H atoms. Skipping. Residue THR 614 is missing expected H atoms. Skipping. Residue LEU 615 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue THR 626 is missing expected H atoms. Skipping. Residue ALA 638 is missing expected H atoms. Skipping. Residue LYS 643 is missing expected H atoms. Skipping. Residue LYS 645 is missing expected H atoms. Skipping. Residue LEU 648 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LEU 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue VAL 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 672 is missing expected H atoms. Skipping. Residue SER 673 is missing expected H atoms. Skipping. Residue THR 675 is missing expected H atoms. Skipping. Residue VAL 676 is missing expected H atoms. Skipping. Residue SER 679 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 690 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue ALA 698 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue VAL 727 is missing expected H atoms. Skipping. Residue SER 728 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue ILE 754 is missing expected H atoms. Skipping. Residue LEU 764 is missing expected H atoms. Skipping. Residue THR 765 is missing expected H atoms. Skipping. Residue LEU 767 is missing expected H atoms. Skipping. Residue VAL 769 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 775 is missing expected H atoms. Skipping. Residue LEU 776 is missing expected H atoms. Skipping. Residue SER 777 is missing expected H atoms. Skipping. Residue ALA 791 is missing expected H atoms. Skipping. Residue ALA 808 is missing expected H atoms. Skipping. Residue MET 810 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ALA 833 is missing expected H atoms. Skipping. Residue ALA 834 is missing expected H atoms. Skipping. Residue THR 835 is missing expected H atoms. Skipping. Residue VAL 839 is missing expected H atoms. Skipping. Residue ALA 843 is missing expected H atoms. Skipping. Residue LEU 917 is missing expected H atoms. Skipping. Residue SER 919 is missing expected H atoms. Skipping. Residue TYR 920 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue ALA 962 is missing expected H atoms. Skipping. Residue THR 980 is missing expected H atoms. Skipping. Residue LYS 1009 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1020 is missing expected H atoms. Skipping. Residue THR 1035 is missing expected H atoms. Skipping. Residue VAL 1036 is missing expected H atoms. Skipping. Residue ILE 1050 is missing expected H atoms. Skipping. Residue SER 1082 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue THR 1101 is missing expected H atoms. Skipping. Residue LEU 1104 is missing expected H atoms. Skipping. Residue SER 1141 is missing expected H atoms. Skipping. Residue LYS 1143 is missing expected H atoms. Skipping. Residue MET 1166 is missing expected H atoms. Skipping. Residue LYS 1174 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue ALA 1199 is missing expected H atoms. Skipping. Residue LYS 1216 is missing expected H atoms. Skipping. Residue SER 1227 is missing expected H atoms. Skipping. Residue LYS 1253 is missing expected H atoms. Skipping. Residue SER 1257 is missing expected H atoms. Skipping. Residue SER 1287 is missing expected H atoms. Skipping. Residue LYS 1307 is missing expected H atoms. Skipping. Residue LYS 1318 is missing expected H atoms. Skipping. Residue LYS 1319 is missing expected H atoms. Skipping. Residue LYS 1329 is missing expected H atoms. Skipping. Residue ALA 1373 is missing expected H atoms. Skipping. Residue LYS 1390 is missing expected H atoms. Skipping. Residue MET 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue TYR 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue THR 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue THR 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue VAL 380 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue TYR 395 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue VAL 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue ALA 454 is missing expected H atoms. Skipping. Residue ALA 455 is missing expected H atoms. Skipping. Residue SER 456 is missing expected H atoms. Skipping. Residue ALA 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue SER 479 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue ALA 504 is missing expected H atoms. Skipping. Residue SER 512 is missing expected H atoms. Skipping. Residue MET 513 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue ALA 526 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 534 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue LEU 552 is missing expected H atoms. Skipping. Residue ALA 584 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue SER 598 is missing expected H atoms. Skipping. Residue ALA 601 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue MET 626 is missing expected H atoms. Skipping. Residue LYS 634 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue LEU 643 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue LEU 647 is missing expected H atoms. Skipping. Residue LYS 648 is missing expected H atoms. Skipping. Residue LEU 649 is missing expected H atoms. Skipping. Residue ILE 653 is missing expected H atoms. Skipping. Residue MET 654 is missing expected H atoms. Skipping. Residue ILE 660 is missing expected H atoms. Skipping. Residue ALA 667 is missing expected H atoms. Skipping. Residue THR 683 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue MET 709 is missing expected H atoms. Skipping. Residue LYS 719 is missing expected H atoms. Skipping. Residue SER 720 is missing expected H atoms. Skipping. Residue LEU 722 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue VAL 739 is missing expected H atoms. Skipping. Residue LYS 742 is missing expected H atoms. Skipping. Residue LYS 763 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue SER 807 is missing expected H atoms. Skipping. Residue ALA 820 is missing expected H atoms. Skipping. Residue ALA 826 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LEU 833 is missing expected H atoms. Skipping. Residue LEU 836 is missing expected H atoms. Skipping. Residue SER 839 is missing expected H atoms. Skipping. Residue ALA 846 is missing expected H atoms. Skipping. Residue MET 860 is missing expected H atoms. Skipping. Residue LYS 873 is missing expected H atoms. Skipping. Residue SER 891 is missing expected H atoms. Skipping. Residue ILE 892 is missing expected H atoms. Skipping. Residue SER 906 is missing expected H atoms. Skipping. Residue ILE 949 is missing expected H atoms. Skipping. Residue SER 972 is missing expected H atoms. Skipping. Residue LEU 1019 is missing expected H atoms. Skipping. Residue LEU 1022 is missing expected H atoms. Skipping. Residue SER 1070 is missing expected H atoms. Skipping. Residue ILE 1074 is missing expected H atoms. Skipping. Residue LYS 1078 is missing expected H atoms. Skipping. Residue THR 1107 is missing expected H atoms. Skipping. Residue THR 1124 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Residue ALA 1180 is missing expected H atoms. Skipping. Residue VAL 1188 is missing expected H atoms. Skipping. Residue ILE 1217 is missing expected H atoms. Skipping. Residue SER 1219 is missing expected H atoms. Skipping. Residue SER 1221 is missing expected H atoms. Skipping. Residue SER 1223 is missing expected H atoms. Skipping. Residue LYS 1274 is missing expected H atoms. Skipping. Residue SER 1275 is missing expected H atoms. Skipping. Residue MET 1297 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8543 (p0) cc_final: 0.8330 (p0) outliers start: 2 outliers final: 2 residues processed: 68 average time/residue: 0.3785 time to fit residues: 45.7205 Evaluate side-chains 67 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain B residue 1171 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 39 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 0.3980 chunk 130 optimal weight: 8.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.084021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.058858 restraints weight = 185179.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.059860 restraints weight = 77709.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.060153 restraints weight = 43116.322| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15319 Z= 0.141 Angle : 0.458 4.923 20774 Z= 0.258 Chirality : 0.034 0.128 2369 Planarity : 0.004 0.054 2618 Dihedral : 14.927 173.215 2834 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.75 % Rotamer: Outliers : 0.41 % Allowed : 6.94 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.19), residues: 2151 helix: 3.14 (0.13), residues: 1606 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 679 HIS 0.003 0.001 HIS A1061 PHE 0.012 0.001 PHE A 736 TYR 0.010 0.001 TYR A1297 ARG 0.003 0.000 ARG B 616 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 1178) hydrogen bonds : angle 3.60017 ( 3465) covalent geometry : bond 0.00301 (15319) covalent geometry : angle 0.45753 (20774) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue TYR 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue ILE 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 200 is missing expected H atoms. Skipping. Residue MET 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 239 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue VAL 246 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue MET 270 is missing expected H atoms. Skipping. Residue ILE 272 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue ALA 297 is missing expected H atoms. Skipping. Residue ILE 301 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 400 is missing expected H atoms. Skipping. Residue THR 402 is missing expected H atoms. Skipping. Residue LYS 404 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue MET 420 is missing expected H atoms. Skipping. Residue SER 428 is missing expected H atoms. Skipping. Residue MET 429 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue ALA 464 is missing expected H atoms. Skipping. Residue ALA 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue TYR 471 is missing expected H atoms. Skipping. Residue VAL 476 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue ILE 504 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue SER 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue TYR 513 is missing expected H atoms. Skipping. Residue ALA 514 is missing expected H atoms. Skipping. Residue THR 515 is missing expected H atoms. Skipping. Residue VAL 517 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue THR 519 is missing expected H atoms. Skipping. Residue ILE 520 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue SER 523 is missing expected H atoms. Skipping. Residue MET 524 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LYS 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue SER 540 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue SER 545 is missing expected H atoms. Skipping. Residue SER 551 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue MET 559 is missing expected H atoms. Skipping. Residue LYS 563 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue SER 567 is missing expected H atoms. Skipping. Residue SER 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue MET 575 is missing expected H atoms. Skipping. Residue THR 582 is missing expected H atoms. Skipping. Residue MET 583 is missing expected H atoms. Skipping. Residue SER 586 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue SER 613 is missing expected H atoms. Skipping. Residue THR 614 is missing expected H atoms. Skipping. Residue LEU 615 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue THR 626 is missing expected H atoms. Skipping. Residue ALA 638 is missing expected H atoms. Skipping. Residue LYS 643 is missing expected H atoms. Skipping. Residue LYS 645 is missing expected H atoms. Skipping. Residue LEU 648 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LEU 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue VAL 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 672 is missing expected H atoms. Skipping. Residue SER 673 is missing expected H atoms. Skipping. Residue THR 675 is missing expected H atoms. Skipping. Residue VAL 676 is missing expected H atoms. Skipping. Residue SER 679 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 690 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue ALA 698 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue VAL 727 is missing expected H atoms. Skipping. Residue SER 728 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue ILE 754 is missing expected H atoms. Skipping. Residue LEU 764 is missing expected H atoms. Skipping. Residue THR 765 is missing expected H atoms. Skipping. Residue LEU 767 is missing expected H atoms. Skipping. Residue VAL 769 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 775 is missing expected H atoms. Skipping. Residue LEU 776 is missing expected H atoms. Skipping. Residue SER 777 is missing expected H atoms. Skipping. Residue ALA 791 is missing expected H atoms. Skipping. Residue ALA 808 is missing expected H atoms. Skipping. Residue MET 810 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ALA 833 is missing expected H atoms. Skipping. Residue ALA 834 is missing expected H atoms. Skipping. Residue THR 835 is missing expected H atoms. Skipping. Residue VAL 839 is missing expected H atoms. Skipping. Residue ALA 843 is missing expected H atoms. Skipping. Residue LEU 917 is missing expected H atoms. Skipping. Residue SER 919 is missing expected H atoms. Skipping. Residue TYR 920 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue ALA 962 is missing expected H atoms. Skipping. Residue THR 980 is missing expected H atoms. Skipping. Residue LYS 1009 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1020 is missing expected H atoms. Skipping. Residue THR 1035 is missing expected H atoms. Skipping. Residue VAL 1036 is missing expected H atoms. Skipping. Residue ILE 1050 is missing expected H atoms. Skipping. Residue SER 1082 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue THR 1101 is missing expected H atoms. Skipping. Residue LEU 1104 is missing expected H atoms. Skipping. Residue SER 1141 is missing expected H atoms. Skipping. Residue LYS 1143 is missing expected H atoms. Skipping. Residue MET 1166 is missing expected H atoms. Skipping. Residue LYS 1174 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue ALA 1199 is missing expected H atoms. Skipping. Residue LYS 1216 is missing expected H atoms. Skipping. Residue SER 1227 is missing expected H atoms. Skipping. Residue LYS 1253 is missing expected H atoms. Skipping. Residue SER 1257 is missing expected H atoms. Skipping. Residue SER 1287 is missing expected H atoms. Skipping. Residue LYS 1307 is missing expected H atoms. Skipping. Residue LYS 1318 is missing expected H atoms. Skipping. Residue LYS 1319 is missing expected H atoms. Skipping. Residue LYS 1329 is missing expected H atoms. Skipping. Residue ALA 1373 is missing expected H atoms. Skipping. Residue LYS 1390 is missing expected H atoms. Skipping. Residue MET 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue TYR 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue THR 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue THR 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue VAL 380 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue TYR 395 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue VAL 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue ALA 454 is missing expected H atoms. Skipping. Residue ALA 455 is missing expected H atoms. Skipping. Residue SER 456 is missing expected H atoms. Skipping. Residue ALA 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue SER 479 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue ALA 504 is missing expected H atoms. Skipping. Residue SER 512 is missing expected H atoms. Skipping. Residue MET 513 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue ALA 526 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 534 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue LEU 552 is missing expected H atoms. Skipping. Residue ALA 584 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue SER 598 is missing expected H atoms. Skipping. Residue ALA 601 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue MET 626 is missing expected H atoms. Skipping. Residue LYS 634 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue LEU 643 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue LEU 647 is missing expected H atoms. Skipping. Residue LYS 648 is missing expected H atoms. Skipping. Residue LEU 649 is missing expected H atoms. Skipping. Residue ILE 653 is missing expected H atoms. Skipping. Residue MET 654 is missing expected H atoms. Skipping. Residue ILE 660 is missing expected H atoms. Skipping. Residue ALA 667 is missing expected H atoms. Skipping. Residue THR 683 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue MET 709 is missing expected H atoms. Skipping. Residue LYS 719 is missing expected H atoms. Skipping. Residue SER 720 is missing expected H atoms. Skipping. Residue LEU 722 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue VAL 739 is missing expected H atoms. Skipping. Residue LYS 742 is missing expected H atoms. Skipping. Residue LYS 763 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue SER 807 is missing expected H atoms. Skipping. Residue ALA 820 is missing expected H atoms. Skipping. Residue ALA 826 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LEU 833 is missing expected H atoms. Skipping. Residue LEU 836 is missing expected H atoms. Skipping. Residue SER 839 is missing expected H atoms. Skipping. Residue ALA 846 is missing expected H atoms. Skipping. Residue MET 860 is missing expected H atoms. Skipping. Residue LYS 873 is missing expected H atoms. Skipping. Residue SER 891 is missing expected H atoms. Skipping. Residue ILE 892 is missing expected H atoms. Skipping. Residue SER 906 is missing expected H atoms. Skipping. Residue ILE 949 is missing expected H atoms. Skipping. Residue SER 972 is missing expected H atoms. Skipping. Residue LEU 1019 is missing expected H atoms. Skipping. Residue LEU 1022 is missing expected H atoms. Skipping. Residue SER 1070 is missing expected H atoms. Skipping. Residue ILE 1074 is missing expected H atoms. Skipping. Residue LYS 1078 is missing expected H atoms. Skipping. Residue THR 1107 is missing expected H atoms. Skipping. Residue THR 1124 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Residue ALA 1180 is missing expected H atoms. Skipping. Residue VAL 1188 is missing expected H atoms. Skipping. Residue ILE 1217 is missing expected H atoms. Skipping. Residue SER 1219 is missing expected H atoms. Skipping. Residue SER 1221 is missing expected H atoms. Skipping. Residue SER 1223 is missing expected H atoms. Skipping. Residue LYS 1274 is missing expected H atoms. Skipping. Residue SER 1275 is missing expected H atoms. Skipping. Residue MET 1297 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8545 (p0) cc_final: 0.8320 (p0) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.4141 time to fit residues: 52.3820 Evaluate side-chains 69 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain B residue 1171 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 65 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 205 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1081 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.083136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.056551 restraints weight = 188221.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.058340 restraints weight = 72017.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.059416 restraints weight = 39971.237| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15319 Z= 0.194 Angle : 0.500 6.092 20774 Z= 0.284 Chirality : 0.035 0.136 2369 Planarity : 0.004 0.054 2618 Dihedral : 14.763 175.641 2834 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 0.58 % Allowed : 7.77 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.18), residues: 2151 helix: 2.97 (0.13), residues: 1599 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1385 HIS 0.004 0.001 HIS B1270 PHE 0.016 0.001 PHE A 736 TYR 0.012 0.001 TYR A1297 ARG 0.002 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 1178) hydrogen bonds : angle 3.83482 ( 3465) covalent geometry : bond 0.00417 (15319) covalent geometry : angle 0.49956 (20774) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue TYR 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue ILE 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 200 is missing expected H atoms. Skipping. Residue MET 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 239 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue VAL 246 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue MET 270 is missing expected H atoms. Skipping. Residue ILE 272 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue ALA 297 is missing expected H atoms. Skipping. Residue ILE 301 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 400 is missing expected H atoms. Skipping. Residue THR 402 is missing expected H atoms. Skipping. Residue LYS 404 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue MET 420 is missing expected H atoms. Skipping. Residue SER 428 is missing expected H atoms. Skipping. Residue MET 429 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue ALA 464 is missing expected H atoms. Skipping. Residue ALA 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue TYR 471 is missing expected H atoms. Skipping. Residue VAL 476 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue ILE 504 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue SER 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue TYR 513 is missing expected H atoms. Skipping. Residue ALA 514 is missing expected H atoms. Skipping. Residue THR 515 is missing expected H atoms. Skipping. Residue VAL 517 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue THR 519 is missing expected H atoms. Skipping. Residue ILE 520 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue SER 523 is missing expected H atoms. Skipping. Residue MET 524 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LYS 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue SER 540 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue SER 545 is missing expected H atoms. Skipping. Residue SER 551 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue MET 559 is missing expected H atoms. Skipping. Residue LYS 563 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue SER 567 is missing expected H atoms. Skipping. Residue SER 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue MET 575 is missing expected H atoms. Skipping. Residue THR 582 is missing expected H atoms. Skipping. Residue MET 583 is missing expected H atoms. Skipping. Residue SER 586 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue SER 613 is missing expected H atoms. Skipping. Residue THR 614 is missing expected H atoms. Skipping. Residue LEU 615 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue THR 626 is missing expected H atoms. Skipping. Residue ALA 638 is missing expected H atoms. Skipping. Residue LYS 643 is missing expected H atoms. Skipping. Residue LYS 645 is missing expected H atoms. Skipping. Residue LEU 648 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LEU 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue VAL 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 672 is missing expected H atoms. Skipping. Residue SER 673 is missing expected H atoms. Skipping. Residue THR 675 is missing expected H atoms. Skipping. Residue VAL 676 is missing expected H atoms. Skipping. Residue SER 679 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 690 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue ALA 698 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue VAL 727 is missing expected H atoms. Skipping. Residue SER 728 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue ILE 754 is missing expected H atoms. Skipping. Residue LEU 764 is missing expected H atoms. Skipping. Residue THR 765 is missing expected H atoms. Skipping. Residue LEU 767 is missing expected H atoms. Skipping. Residue VAL 769 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 775 is missing expected H atoms. Skipping. Residue LEU 776 is missing expected H atoms. Skipping. Residue SER 777 is missing expected H atoms. Skipping. Residue ALA 791 is missing expected H atoms. Skipping. Residue ALA 808 is missing expected H atoms. Skipping. Residue MET 810 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ALA 833 is missing expected H atoms. Skipping. Residue ALA 834 is missing expected H atoms. Skipping. Residue THR 835 is missing expected H atoms. Skipping. Residue VAL 839 is missing expected H atoms. Skipping. Residue ALA 843 is missing expected H atoms. Skipping. Residue LEU 917 is missing expected H atoms. Skipping. Residue SER 919 is missing expected H atoms. Skipping. Residue TYR 920 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue ALA 962 is missing expected H atoms. Skipping. Residue THR 980 is missing expected H atoms. Skipping. Residue LYS 1009 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1020 is missing expected H atoms. Skipping. Residue THR 1035 is missing expected H atoms. Skipping. Residue VAL 1036 is missing expected H atoms. Skipping. Residue ILE 1050 is missing expected H atoms. Skipping. Residue SER 1082 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue THR 1101 is missing expected H atoms. Skipping. Residue LEU 1104 is missing expected H atoms. Skipping. Residue SER 1141 is missing expected H atoms. Skipping. Residue LYS 1143 is missing expected H atoms. Skipping. Residue MET 1166 is missing expected H atoms. Skipping. Residue LYS 1174 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue ALA 1199 is missing expected H atoms. Skipping. Residue LYS 1216 is missing expected H atoms. Skipping. Residue SER 1227 is missing expected H atoms. Skipping. Residue LYS 1253 is missing expected H atoms. Skipping. Residue SER 1257 is missing expected H atoms. Skipping. Residue SER 1287 is missing expected H atoms. Skipping. Residue LYS 1307 is missing expected H atoms. Skipping. Residue LYS 1318 is missing expected H atoms. Skipping. Residue LYS 1319 is missing expected H atoms. Skipping. Residue LYS 1329 is missing expected H atoms. Skipping. Residue ALA 1373 is missing expected H atoms. Skipping. Residue LYS 1390 is missing expected H atoms. Skipping. Residue MET 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue TYR 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue THR 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue THR 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue VAL 380 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue TYR 395 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue VAL 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue ALA 454 is missing expected H atoms. Skipping. Residue ALA 455 is missing expected H atoms. Skipping. Residue SER 456 is missing expected H atoms. Skipping. Residue ALA 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue SER 479 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue ALA 504 is missing expected H atoms. Skipping. Residue SER 512 is missing expected H atoms. Skipping. Residue MET 513 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue ALA 526 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 534 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue LEU 552 is missing expected H atoms. Skipping. Residue ALA 584 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue SER 598 is missing expected H atoms. Skipping. Residue ALA 601 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue MET 626 is missing expected H atoms. Skipping. Residue LYS 634 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue LEU 643 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue LEU 647 is missing expected H atoms. Skipping. Residue LYS 648 is missing expected H atoms. Skipping. Residue LEU 649 is missing expected H atoms. Skipping. Residue ILE 653 is missing expected H atoms. Skipping. Residue MET 654 is missing expected H atoms. Skipping. Residue ILE 660 is missing expected H atoms. Skipping. Residue ALA 667 is missing expected H atoms. Skipping. Residue THR 683 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue MET 709 is missing expected H atoms. Skipping. Residue LYS 719 is missing expected H atoms. Skipping. Residue SER 720 is missing expected H atoms. Skipping. Residue LEU 722 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue VAL 739 is missing expected H atoms. Skipping. Residue LYS 742 is missing expected H atoms. Skipping. Residue LYS 763 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue SER 807 is missing expected H atoms. Skipping. Residue ALA 820 is missing expected H atoms. Skipping. Residue ALA 826 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LEU 833 is missing expected H atoms. Skipping. Residue LEU 836 is missing expected H atoms. Skipping. Residue SER 839 is missing expected H atoms. Skipping. Residue ALA 846 is missing expected H atoms. Skipping. Residue MET 860 is missing expected H atoms. Skipping. Residue LYS 873 is missing expected H atoms. Skipping. Residue SER 891 is missing expected H atoms. Skipping. Residue ILE 892 is missing expected H atoms. Skipping. Residue SER 906 is missing expected H atoms. Skipping. Residue ILE 949 is missing expected H atoms. Skipping. Residue SER 972 is missing expected H atoms. Skipping. Residue LEU 1019 is missing expected H atoms. Skipping. Residue LEU 1022 is missing expected H atoms. Skipping. Residue SER 1070 is missing expected H atoms. Skipping. Residue ILE 1074 is missing expected H atoms. Skipping. Residue LYS 1078 is missing expected H atoms. Skipping. Residue THR 1107 is missing expected H atoms. Skipping. Residue THR 1124 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Residue ALA 1180 is missing expected H atoms. Skipping. Residue VAL 1188 is missing expected H atoms. Skipping. Residue ILE 1217 is missing expected H atoms. Skipping. Residue SER 1219 is missing expected H atoms. Skipping. Residue SER 1221 is missing expected H atoms. Skipping. Residue SER 1223 is missing expected H atoms. Skipping. Residue LYS 1274 is missing expected H atoms. Skipping. Residue SER 1275 is missing expected H atoms. Skipping. Residue MET 1297 is missing expected H atoms. Skipping. Evaluate side-chains 71 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASP cc_start: 0.8503 (p0) cc_final: 0.8266 (p0) outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.3814 time to fit residues: 47.9180 Evaluate side-chains 69 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain B residue 1171 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 80 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 89 optimal weight: 8.9990 chunk 33 optimal weight: 0.0980 chunk 172 optimal weight: 0.9980 chunk 117 optimal weight: 30.0000 chunk 159 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.083391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.058135 restraints weight = 186508.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.059344 restraints weight = 78882.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.059420 restraints weight = 44258.395| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15319 Z= 0.163 Angle : 0.477 4.840 20774 Z= 0.271 Chirality : 0.035 0.143 2369 Planarity : 0.003 0.053 2618 Dihedral : 14.659 177.511 2834 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 0.66 % Allowed : 7.93 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.19), residues: 2151 helix: 3.06 (0.13), residues: 1603 sheet: None (None), residues: 0 loop : -1.25 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 679 HIS 0.003 0.001 HIS B1270 PHE 0.014 0.001 PHE A 736 TYR 0.011 0.001 TYR A1297 ARG 0.002 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 1178) hydrogen bonds : angle 3.69474 ( 3465) covalent geometry : bond 0.00350 (15319) covalent geometry : angle 0.47678 (20774) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue TYR 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue ILE 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 200 is missing expected H atoms. Skipping. Residue MET 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 239 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue VAL 246 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue MET 270 is missing expected H atoms. Skipping. Residue ILE 272 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue ALA 297 is missing expected H atoms. Skipping. Residue ILE 301 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 400 is missing expected H atoms. Skipping. Residue THR 402 is missing expected H atoms. Skipping. Residue LYS 404 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue MET 420 is missing expected H atoms. Skipping. Residue SER 428 is missing expected H atoms. Skipping. Residue MET 429 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue ALA 464 is missing expected H atoms. Skipping. Residue ALA 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue TYR 471 is missing expected H atoms. Skipping. Residue VAL 476 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue ILE 504 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue SER 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue TYR 513 is missing expected H atoms. Skipping. Residue ALA 514 is missing expected H atoms. Skipping. Residue THR 515 is missing expected H atoms. Skipping. Residue VAL 517 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue THR 519 is missing expected H atoms. Skipping. Residue ILE 520 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue SER 523 is missing expected H atoms. Skipping. Residue MET 524 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LYS 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue SER 540 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue SER 545 is missing expected H atoms. Skipping. Residue SER 551 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue MET 559 is missing expected H atoms. Skipping. Residue LYS 563 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue SER 567 is missing expected H atoms. Skipping. Residue SER 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue MET 575 is missing expected H atoms. Skipping. Residue THR 582 is missing expected H atoms. Skipping. Residue MET 583 is missing expected H atoms. Skipping. Residue SER 586 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue SER 613 is missing expected H atoms. Skipping. Residue THR 614 is missing expected H atoms. Skipping. Residue LEU 615 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue THR 626 is missing expected H atoms. Skipping. Residue ALA 638 is missing expected H atoms. Skipping. Residue LYS 643 is missing expected H atoms. Skipping. Residue LYS 645 is missing expected H atoms. Skipping. Residue LEU 648 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LEU 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue VAL 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 672 is missing expected H atoms. Skipping. Residue SER 673 is missing expected H atoms. Skipping. Residue THR 675 is missing expected H atoms. Skipping. Residue VAL 676 is missing expected H atoms. Skipping. Residue SER 679 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 690 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue ALA 698 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue VAL 727 is missing expected H atoms. Skipping. Residue SER 728 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue ILE 754 is missing expected H atoms. Skipping. Residue LEU 764 is missing expected H atoms. Skipping. Residue THR 765 is missing expected H atoms. Skipping. Residue LEU 767 is missing expected H atoms. Skipping. Residue VAL 769 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 775 is missing expected H atoms. Skipping. Residue LEU 776 is missing expected H atoms. Skipping. Residue SER 777 is missing expected H atoms. Skipping. Residue ALA 791 is missing expected H atoms. Skipping. Residue ALA 808 is missing expected H atoms. Skipping. Residue MET 810 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ALA 833 is missing expected H atoms. Skipping. Residue ALA 834 is missing expected H atoms. Skipping. Residue THR 835 is missing expected H atoms. Skipping. Residue VAL 839 is missing expected H atoms. Skipping. Residue ALA 843 is missing expected H atoms. Skipping. Residue LEU 917 is missing expected H atoms. Skipping. Residue SER 919 is missing expected H atoms. Skipping. Residue TYR 920 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue ALA 962 is missing expected H atoms. Skipping. Residue THR 980 is missing expected H atoms. Skipping. Residue LYS 1009 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1020 is missing expected H atoms. Skipping. Residue THR 1035 is missing expected H atoms. Skipping. Residue VAL 1036 is missing expected H atoms. Skipping. Residue ILE 1050 is missing expected H atoms. Skipping. Residue SER 1082 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue THR 1101 is missing expected H atoms. Skipping. Residue LEU 1104 is missing expected H atoms. Skipping. Residue SER 1141 is missing expected H atoms. Skipping. Residue LYS 1143 is missing expected H atoms. Skipping. Residue MET 1166 is missing expected H atoms. Skipping. Residue LYS 1174 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue ALA 1199 is missing expected H atoms. Skipping. Residue LYS 1216 is missing expected H atoms. Skipping. Residue SER 1227 is missing expected H atoms. Skipping. Residue LYS 1253 is missing expected H atoms. Skipping. Residue SER 1257 is missing expected H atoms. Skipping. Residue SER 1287 is missing expected H atoms. Skipping. Residue LYS 1307 is missing expected H atoms. Skipping. Residue LYS 1318 is missing expected H atoms. Skipping. Residue LYS 1319 is missing expected H atoms. Skipping. Residue LYS 1329 is missing expected H atoms. Skipping. Residue ALA 1373 is missing expected H atoms. Skipping. Residue LYS 1390 is missing expected H atoms. Skipping. Residue MET 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue TYR 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue THR 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue THR 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue VAL 380 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue TYR 395 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue VAL 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue ALA 454 is missing expected H atoms. Skipping. Residue ALA 455 is missing expected H atoms. Skipping. Residue SER 456 is missing expected H atoms. Skipping. Residue ALA 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue SER 479 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue ALA 504 is missing expected H atoms. Skipping. Residue SER 512 is missing expected H atoms. Skipping. Residue MET 513 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue ALA 526 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 534 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue LEU 552 is missing expected H atoms. Skipping. Residue ALA 584 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue SER 598 is missing expected H atoms. Skipping. Residue ALA 601 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue MET 626 is missing expected H atoms. Skipping. Residue LYS 634 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue LEU 643 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue LEU 647 is missing expected H atoms. Skipping. Residue LYS 648 is missing expected H atoms. Skipping. Residue LEU 649 is missing expected H atoms. Skipping. Residue ILE 653 is missing expected H atoms. Skipping. Residue MET 654 is missing expected H atoms. Skipping. Residue ILE 660 is missing expected H atoms. Skipping. Residue ALA 667 is missing expected H atoms. Skipping. Residue THR 683 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue MET 709 is missing expected H atoms. Skipping. Residue LYS 719 is missing expected H atoms. Skipping. Residue SER 720 is missing expected H atoms. Skipping. Residue LEU 722 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue VAL 739 is missing expected H atoms. Skipping. Residue LYS 742 is missing expected H atoms. Skipping. Residue LYS 763 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue SER 807 is missing expected H atoms. Skipping. Residue ALA 820 is missing expected H atoms. Skipping. Residue ALA 826 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LEU 833 is missing expected H atoms. Skipping. Residue LEU 836 is missing expected H atoms. Skipping. Residue SER 839 is missing expected H atoms. Skipping. Residue ALA 846 is missing expected H atoms. Skipping. Residue MET 860 is missing expected H atoms. Skipping. Residue LYS 873 is missing expected H atoms. Skipping. Residue SER 891 is missing expected H atoms. Skipping. Residue ILE 892 is missing expected H atoms. Skipping. Residue SER 906 is missing expected H atoms. Skipping. Residue ILE 949 is missing expected H atoms. Skipping. Residue SER 972 is missing expected H atoms. Skipping. Residue LEU 1019 is missing expected H atoms. Skipping. Residue LEU 1022 is missing expected H atoms. Skipping. Residue SER 1070 is missing expected H atoms. Skipping. Residue ILE 1074 is missing expected H atoms. Skipping. Residue LYS 1078 is missing expected H atoms. Skipping. Residue THR 1107 is missing expected H atoms. Skipping. Residue THR 1124 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Residue ALA 1180 is missing expected H atoms. Skipping. Residue VAL 1188 is missing expected H atoms. Skipping. Residue ILE 1217 is missing expected H atoms. Skipping. Residue SER 1219 is missing expected H atoms. Skipping. Residue SER 1221 is missing expected H atoms. Skipping. Residue SER 1223 is missing expected H atoms. Skipping. Residue LYS 1274 is missing expected H atoms. Skipping. Residue SER 1275 is missing expected H atoms. Skipping. Residue MET 1297 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8885 (mp) REVERT: B 170 ASP cc_start: 0.8590 (p0) cc_final: 0.8356 (p0) outliers start: 8 outliers final: 6 residues processed: 72 average time/residue: 0.3718 time to fit residues: 47.2563 Evaluate side-chains 71 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1171 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 116 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 110 optimal weight: 0.0470 chunk 38 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.084854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.059119 restraints weight = 188639.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.059936 restraints weight = 78932.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.060210 restraints weight = 45409.074| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15319 Z= 0.122 Angle : 0.450 6.346 20774 Z= 0.253 Chirality : 0.034 0.130 2369 Planarity : 0.003 0.053 2618 Dihedral : 14.450 179.483 2834 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 0.50 % Allowed : 8.51 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.19), residues: 2151 helix: 3.27 (0.13), residues: 1613 sheet: None (None), residues: 0 loop : -1.18 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 679 HIS 0.003 0.001 HIS A1061 PHE 0.011 0.001 PHE B 962 TYR 0.009 0.001 TYR A1297 ARG 0.002 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 1178) hydrogen bonds : angle 3.43339 ( 3465) covalent geometry : bond 0.00258 (15319) covalent geometry : angle 0.45019 (20774) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue TYR 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue ILE 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 200 is missing expected H atoms. Skipping. Residue MET 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 239 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue VAL 246 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue MET 270 is missing expected H atoms. Skipping. Residue ILE 272 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue ALA 297 is missing expected H atoms. Skipping. Residue ILE 301 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 400 is missing expected H atoms. Skipping. Residue THR 402 is missing expected H atoms. Skipping. Residue LYS 404 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue MET 420 is missing expected H atoms. Skipping. Residue SER 428 is missing expected H atoms. Skipping. Residue MET 429 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue ALA 464 is missing expected H atoms. Skipping. Residue ALA 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue TYR 471 is missing expected H atoms. Skipping. Residue VAL 476 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue ILE 504 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue SER 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue TYR 513 is missing expected H atoms. Skipping. Residue ALA 514 is missing expected H atoms. Skipping. Residue THR 515 is missing expected H atoms. Skipping. Residue VAL 517 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue THR 519 is missing expected H atoms. Skipping. Residue ILE 520 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue SER 523 is missing expected H atoms. Skipping. Residue MET 524 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LYS 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue SER 540 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue SER 545 is missing expected H atoms. Skipping. Residue SER 551 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue MET 559 is missing expected H atoms. Skipping. Residue LYS 563 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue SER 567 is missing expected H atoms. Skipping. Residue SER 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue MET 575 is missing expected H atoms. Skipping. Residue THR 582 is missing expected H atoms. Skipping. Residue MET 583 is missing expected H atoms. Skipping. Residue SER 586 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue SER 613 is missing expected H atoms. Skipping. Residue THR 614 is missing expected H atoms. Skipping. Residue LEU 615 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue THR 626 is missing expected H atoms. Skipping. Residue ALA 638 is missing expected H atoms. Skipping. Residue LYS 643 is missing expected H atoms. Skipping. Residue LYS 645 is missing expected H atoms. Skipping. Residue LEU 648 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LEU 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue VAL 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 672 is missing expected H atoms. Skipping. Residue SER 673 is missing expected H atoms. Skipping. Residue THR 675 is missing expected H atoms. Skipping. Residue VAL 676 is missing expected H atoms. Skipping. Residue SER 679 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 690 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue ALA 698 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue VAL 727 is missing expected H atoms. Skipping. Residue SER 728 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue ILE 754 is missing expected H atoms. Skipping. Residue LEU 764 is missing expected H atoms. Skipping. Residue THR 765 is missing expected H atoms. Skipping. Residue LEU 767 is missing expected H atoms. Skipping. Residue VAL 769 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 775 is missing expected H atoms. Skipping. Residue LEU 776 is missing expected H atoms. Skipping. Residue SER 777 is missing expected H atoms. Skipping. Residue ALA 791 is missing expected H atoms. Skipping. Residue ALA 808 is missing expected H atoms. Skipping. Residue MET 810 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ALA 833 is missing expected H atoms. Skipping. Residue ALA 834 is missing expected H atoms. Skipping. Residue THR 835 is missing expected H atoms. Skipping. Residue VAL 839 is missing expected H atoms. Skipping. Residue ALA 843 is missing expected H atoms. Skipping. Residue LEU 917 is missing expected H atoms. Skipping. Residue SER 919 is missing expected H atoms. Skipping. Residue TYR 920 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue ALA 962 is missing expected H atoms. Skipping. Residue THR 980 is missing expected H atoms. Skipping. Residue LYS 1009 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1020 is missing expected H atoms. Skipping. Residue THR 1035 is missing expected H atoms. Skipping. Residue VAL 1036 is missing expected H atoms. Skipping. Residue ILE 1050 is missing expected H atoms. Skipping. Residue SER 1082 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue THR 1101 is missing expected H atoms. Skipping. Residue LEU 1104 is missing expected H atoms. Skipping. Residue SER 1141 is missing expected H atoms. Skipping. Residue LYS 1143 is missing expected H atoms. Skipping. Residue MET 1166 is missing expected H atoms. Skipping. Residue LYS 1174 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue ALA 1199 is missing expected H atoms. Skipping. Residue LYS 1216 is missing expected H atoms. Skipping. Residue SER 1227 is missing expected H atoms. Skipping. Residue LYS 1253 is missing expected H atoms. Skipping. Residue SER 1257 is missing expected H atoms. Skipping. Residue SER 1287 is missing expected H atoms. Skipping. Residue LYS 1307 is missing expected H atoms. Skipping. Residue LYS 1318 is missing expected H atoms. Skipping. Residue LYS 1319 is missing expected H atoms. Skipping. Residue LYS 1329 is missing expected H atoms. Skipping. Residue ALA 1373 is missing expected H atoms. Skipping. Residue LYS 1390 is missing expected H atoms. Skipping. Residue MET 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue TYR 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue THR 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue THR 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue VAL 380 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue TYR 395 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue VAL 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue ALA 454 is missing expected H atoms. Skipping. Residue ALA 455 is missing expected H atoms. Skipping. Residue SER 456 is missing expected H atoms. Skipping. Residue ALA 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue SER 479 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue ALA 504 is missing expected H atoms. Skipping. Residue SER 512 is missing expected H atoms. Skipping. Residue MET 513 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue ALA 526 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 534 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue LEU 552 is missing expected H atoms. Skipping. Residue ALA 584 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue SER 598 is missing expected H atoms. Skipping. Residue ALA 601 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue MET 626 is missing expected H atoms. Skipping. Residue LYS 634 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue LEU 643 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue LEU 647 is missing expected H atoms. Skipping. Residue LYS 648 is missing expected H atoms. Skipping. Residue LEU 649 is missing expected H atoms. Skipping. Residue ILE 653 is missing expected H atoms. Skipping. Residue MET 654 is missing expected H atoms. Skipping. Residue ILE 660 is missing expected H atoms. Skipping. Residue ALA 667 is missing expected H atoms. Skipping. Residue THR 683 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue MET 709 is missing expected H atoms. Skipping. Residue LYS 719 is missing expected H atoms. Skipping. Residue SER 720 is missing expected H atoms. Skipping. Residue LEU 722 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue VAL 739 is missing expected H atoms. Skipping. Residue LYS 742 is missing expected H atoms. Skipping. Residue LYS 763 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue SER 807 is missing expected H atoms. Skipping. Residue ALA 820 is missing expected H atoms. Skipping. Residue ALA 826 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LEU 833 is missing expected H atoms. Skipping. Residue LEU 836 is missing expected H atoms. Skipping. Residue SER 839 is missing expected H atoms. Skipping. Residue ALA 846 is missing expected H atoms. Skipping. Residue MET 860 is missing expected H atoms. Skipping. Residue LYS 873 is missing expected H atoms. Skipping. Residue SER 891 is missing expected H atoms. Skipping. Residue ILE 892 is missing expected H atoms. Skipping. Residue SER 906 is missing expected H atoms. Skipping. Residue ILE 949 is missing expected H atoms. Skipping. Residue SER 972 is missing expected H atoms. Skipping. Residue LEU 1019 is missing expected H atoms. Skipping. Residue LEU 1022 is missing expected H atoms. Skipping. Residue SER 1070 is missing expected H atoms. Skipping. Residue ILE 1074 is missing expected H atoms. Skipping. Residue LYS 1078 is missing expected H atoms. Skipping. Residue THR 1107 is missing expected H atoms. Skipping. Residue THR 1124 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Residue ALA 1180 is missing expected H atoms. Skipping. Residue VAL 1188 is missing expected H atoms. Skipping. Residue ILE 1217 is missing expected H atoms. Skipping. Residue SER 1219 is missing expected H atoms. Skipping. Residue SER 1221 is missing expected H atoms. Skipping. Residue SER 1223 is missing expected H atoms. Skipping. Residue LYS 1274 is missing expected H atoms. Skipping. Residue SER 1275 is missing expected H atoms. Skipping. Residue MET 1297 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8942 (mp) REVERT: B 170 ASP cc_start: 0.8547 (p0) cc_final: 0.8333 (p0) outliers start: 6 outliers final: 4 residues processed: 70 average time/residue: 0.3831 time to fit residues: 47.2788 Evaluate side-chains 69 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1171 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 162 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 210 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 111 optimal weight: 50.0000 chunk 122 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 171 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.083231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.057915 restraints weight = 186043.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.059131 restraints weight = 79866.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.059062 restraints weight = 45922.593| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15319 Z= 0.183 Angle : 0.491 6.960 20774 Z= 0.279 Chirality : 0.035 0.135 2369 Planarity : 0.004 0.052 2618 Dihedral : 14.318 179.806 2834 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 0.41 % Allowed : 9.09 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.19), residues: 2151 helix: 3.15 (0.13), residues: 1607 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 679 HIS 0.005 0.001 HIS B1270 PHE 0.015 0.001 PHE A 736 TYR 0.011 0.001 TYR A1297 ARG 0.002 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 1178) hydrogen bonds : angle 3.67816 ( 3465) covalent geometry : bond 0.00395 (15319) covalent geometry : angle 0.49085 (20774) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue TYR 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue ILE 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 200 is missing expected H atoms. Skipping. Residue MET 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 239 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue VAL 246 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue MET 270 is missing expected H atoms. Skipping. Residue ILE 272 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue ALA 297 is missing expected H atoms. Skipping. Residue ILE 301 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 400 is missing expected H atoms. Skipping. Residue THR 402 is missing expected H atoms. Skipping. Residue LYS 404 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue MET 420 is missing expected H atoms. Skipping. Residue SER 428 is missing expected H atoms. Skipping. Residue MET 429 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue ALA 464 is missing expected H atoms. Skipping. Residue ALA 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue TYR 471 is missing expected H atoms. Skipping. Residue VAL 476 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue ILE 504 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue SER 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue TYR 513 is missing expected H atoms. Skipping. Residue ALA 514 is missing expected H atoms. Skipping. Residue THR 515 is missing expected H atoms. Skipping. Residue VAL 517 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue THR 519 is missing expected H atoms. Skipping. Residue ILE 520 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue SER 523 is missing expected H atoms. Skipping. Residue MET 524 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LYS 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue SER 540 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue SER 545 is missing expected H atoms. Skipping. Residue SER 551 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue MET 559 is missing expected H atoms. Skipping. Residue LYS 563 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue SER 567 is missing expected H atoms. Skipping. Residue SER 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue MET 575 is missing expected H atoms. Skipping. Residue THR 582 is missing expected H atoms. Skipping. Residue MET 583 is missing expected H atoms. Skipping. Residue SER 586 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue SER 613 is missing expected H atoms. Skipping. Residue THR 614 is missing expected H atoms. Skipping. Residue LEU 615 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue THR 626 is missing expected H atoms. Skipping. Residue ALA 638 is missing expected H atoms. Skipping. Residue LYS 643 is missing expected H atoms. Skipping. Residue LYS 645 is missing expected H atoms. Skipping. Residue LEU 648 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LEU 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue VAL 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 672 is missing expected H atoms. Skipping. Residue SER 673 is missing expected H atoms. Skipping. Residue THR 675 is missing expected H atoms. Skipping. Residue VAL 676 is missing expected H atoms. Skipping. Residue SER 679 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 690 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue ALA 698 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue VAL 727 is missing expected H atoms. Skipping. Residue SER 728 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue ILE 754 is missing expected H atoms. Skipping. Residue LEU 764 is missing expected H atoms. Skipping. Residue THR 765 is missing expected H atoms. Skipping. Residue LEU 767 is missing expected H atoms. Skipping. Residue VAL 769 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 775 is missing expected H atoms. Skipping. Residue LEU 776 is missing expected H atoms. Skipping. Residue SER 777 is missing expected H atoms. Skipping. Residue ALA 791 is missing expected H atoms. Skipping. Residue ALA 808 is missing expected H atoms. Skipping. Residue MET 810 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ALA 833 is missing expected H atoms. Skipping. Residue ALA 834 is missing expected H atoms. Skipping. Residue THR 835 is missing expected H atoms. Skipping. Residue VAL 839 is missing expected H atoms. Skipping. Residue ALA 843 is missing expected H atoms. Skipping. Residue LEU 917 is missing expected H atoms. Skipping. Residue SER 919 is missing expected H atoms. Skipping. Residue TYR 920 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue ALA 962 is missing expected H atoms. Skipping. Residue THR 980 is missing expected H atoms. Skipping. Residue LYS 1009 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1020 is missing expected H atoms. Skipping. Residue THR 1035 is missing expected H atoms. Skipping. Residue VAL 1036 is missing expected H atoms. Skipping. Residue ILE 1050 is missing expected H atoms. Skipping. Residue SER 1082 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue THR 1101 is missing expected H atoms. Skipping. Residue LEU 1104 is missing expected H atoms. Skipping. Residue SER 1141 is missing expected H atoms. Skipping. Residue LYS 1143 is missing expected H atoms. Skipping. Residue MET 1166 is missing expected H atoms. Skipping. Residue LYS 1174 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue ALA 1199 is missing expected H atoms. Skipping. Residue LYS 1216 is missing expected H atoms. Skipping. Residue SER 1227 is missing expected H atoms. Skipping. Residue LYS 1253 is missing expected H atoms. Skipping. Residue SER 1257 is missing expected H atoms. Skipping. Residue SER 1287 is missing expected H atoms. Skipping. Residue LYS 1307 is missing expected H atoms. Skipping. Residue LYS 1318 is missing expected H atoms. Skipping. Residue LYS 1319 is missing expected H atoms. Skipping. Residue LYS 1329 is missing expected H atoms. Skipping. Residue ALA 1373 is missing expected H atoms. Skipping. Residue LYS 1390 is missing expected H atoms. Skipping. Residue MET 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue TYR 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue THR 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue THR 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue VAL 380 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue TYR 395 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue VAL 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue ALA 454 is missing expected H atoms. Skipping. Residue ALA 455 is missing expected H atoms. Skipping. Residue SER 456 is missing expected H atoms. Skipping. Residue ALA 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue SER 479 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue ALA 504 is missing expected H atoms. Skipping. Residue SER 512 is missing expected H atoms. Skipping. Residue MET 513 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue ALA 526 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 534 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue LEU 552 is missing expected H atoms. Skipping. Residue ALA 584 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue SER 598 is missing expected H atoms. Skipping. Residue ALA 601 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue MET 626 is missing expected H atoms. Skipping. Residue LYS 634 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue LEU 643 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue LEU 647 is missing expected H atoms. Skipping. Residue LYS 648 is missing expected H atoms. Skipping. Residue LEU 649 is missing expected H atoms. Skipping. Residue ILE 653 is missing expected H atoms. Skipping. Residue MET 654 is missing expected H atoms. Skipping. Residue ILE 660 is missing expected H atoms. Skipping. Residue ALA 667 is missing expected H atoms. Skipping. Residue THR 683 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue MET 709 is missing expected H atoms. Skipping. Residue LYS 719 is missing expected H atoms. Skipping. Residue SER 720 is missing expected H atoms. Skipping. Residue LEU 722 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue VAL 739 is missing expected H atoms. Skipping. Residue LYS 742 is missing expected H atoms. Skipping. Residue LYS 763 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue SER 807 is missing expected H atoms. Skipping. Residue ALA 820 is missing expected H atoms. Skipping. Residue ALA 826 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LEU 833 is missing expected H atoms. Skipping. Residue LEU 836 is missing expected H atoms. Skipping. Residue SER 839 is missing expected H atoms. Skipping. Residue ALA 846 is missing expected H atoms. Skipping. Residue MET 860 is missing expected H atoms. Skipping. Residue LYS 873 is missing expected H atoms. Skipping. Residue SER 891 is missing expected H atoms. Skipping. Residue ILE 892 is missing expected H atoms. Skipping. Residue SER 906 is missing expected H atoms. Skipping. Residue ILE 949 is missing expected H atoms. Skipping. Residue SER 972 is missing expected H atoms. Skipping. Residue LEU 1019 is missing expected H atoms. Skipping. Residue LEU 1022 is missing expected H atoms. Skipping. Residue SER 1070 is missing expected H atoms. Skipping. Residue ILE 1074 is missing expected H atoms. Skipping. Residue LYS 1078 is missing expected H atoms. Skipping. Residue THR 1107 is missing expected H atoms. Skipping. Residue THR 1124 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Residue ALA 1180 is missing expected H atoms. Skipping. Residue VAL 1188 is missing expected H atoms. Skipping. Residue ILE 1217 is missing expected H atoms. Skipping. Residue SER 1219 is missing expected H atoms. Skipping. Residue SER 1221 is missing expected H atoms. Skipping. Residue SER 1223 is missing expected H atoms. Skipping. Residue LYS 1274 is missing expected H atoms. Skipping. Residue SER 1275 is missing expected H atoms. Skipping. Residue MET 1297 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8945 (mp) REVERT: B 170 ASP cc_start: 0.8612 (p0) cc_final: 0.8377 (p0) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.3983 time to fit residues: 48.8014 Evaluate side-chains 69 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1171 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 59 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 21 optimal weight: 30.0000 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.083644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.057821 restraints weight = 189762.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.058953 restraints weight = 81201.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.058982 restraints weight = 48375.781| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15319 Z= 0.157 Angle : 0.472 4.808 20774 Z= 0.267 Chirality : 0.034 0.131 2369 Planarity : 0.003 0.052 2618 Dihedral : 14.159 179.831 2834 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 0.41 % Allowed : 9.17 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.19), residues: 2151 helix: 3.17 (0.13), residues: 1612 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 679 HIS 0.003 0.001 HIS B 71 PHE 0.013 0.001 PHE A 966 TYR 0.010 0.001 TYR A1297 ARG 0.002 0.000 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1178) hydrogen bonds : angle 3.58488 ( 3465) covalent geometry : bond 0.00337 (15319) covalent geometry : angle 0.47160 (20774) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue LEU 54 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 63 is missing expected H atoms. Skipping. Residue ILE 70 is missing expected H atoms. Skipping. Residue VAL 72 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue VAL 83 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue LYS 87 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue TYR 91 is missing expected H atoms. Skipping. Residue VAL 94 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue ILE 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue SER 110 is missing expected H atoms. Skipping. Residue LYS 113 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue ILE 139 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LEU 141 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue ILE 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue ILE 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue ALA 151 is missing expected H atoms. Skipping. Residue VAL 152 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue THR 154 is missing expected H atoms. Skipping. Residue LEU 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue LEU 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue ILE 160 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue LEU 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue MET 200 is missing expected H atoms. Skipping. Residue MET 202 is missing expected H atoms. Skipping. Residue LEU 203 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue ILE 221 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue SER 225 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 239 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue VAL 246 is missing expected H atoms. Skipping. Residue LEU 255 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue ALA 259 is missing expected H atoms. Skipping. Residue LEU 261 is missing expected H atoms. Skipping. Residue LEU 262 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 268 is missing expected H atoms. Skipping. Residue MET 270 is missing expected H atoms. Skipping. Residue ILE 272 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue LYS 277 is missing expected H atoms. Skipping. Residue LEU 278 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue ALA 297 is missing expected H atoms. Skipping. Residue ILE 301 is missing expected H atoms. Skipping. Residue SER 302 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 349 is missing expected H atoms. Skipping. Residue LYS 354 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue LYS 369 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue VAL 377 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 400 is missing expected H atoms. Skipping. Residue THR 402 is missing expected H atoms. Skipping. Residue LYS 404 is missing expected H atoms. Skipping. Residue LYS 409 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LEU 419 is missing expected H atoms. Skipping. Residue MET 420 is missing expected H atoms. Skipping. Residue SER 428 is missing expected H atoms. Skipping. Residue MET 429 is missing expected H atoms. Skipping. Residue ILE 431 is missing expected H atoms. Skipping. Residue LYS 432 is missing expected H atoms. Skipping. Residue SER 437 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 441 is missing expected H atoms. Skipping. Residue ALA 442 is missing expected H atoms. Skipping. Residue THR 444 is missing expected H atoms. Skipping. Residue LEU 446 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 462 is missing expected H atoms. Skipping. Residue ALA 464 is missing expected H atoms. Skipping. Residue ALA 466 is missing expected H atoms. Skipping. Residue VAL 467 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue TYR 471 is missing expected H atoms. Skipping. Residue VAL 476 is missing expected H atoms. Skipping. Residue VAL 484 is missing expected H atoms. Skipping. Residue SER 486 is missing expected H atoms. Skipping. Residue THR 490 is missing expected H atoms. Skipping. Residue ILE 504 is missing expected H atoms. Skipping. Residue LEU 505 is missing expected H atoms. Skipping. Residue SER 508 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue TYR 513 is missing expected H atoms. Skipping. Residue ALA 514 is missing expected H atoms. Skipping. Residue THR 515 is missing expected H atoms. Skipping. Residue VAL 517 is missing expected H atoms. Skipping. Residue LYS 518 is missing expected H atoms. Skipping. Residue THR 519 is missing expected H atoms. Skipping. Residue ILE 520 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue SER 523 is missing expected H atoms. Skipping. Residue MET 524 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue LEU 527 is missing expected H atoms. Skipping. Residue LYS 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue SER 540 is missing expected H atoms. Skipping. Residue THR 541 is missing expected H atoms. Skipping. Residue SER 545 is missing expected H atoms. Skipping. Residue SER 551 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue ILE 553 is missing expected H atoms. Skipping. Residue MET 557 is missing expected H atoms. Skipping. Residue MET 559 is missing expected H atoms. Skipping. Residue LYS 563 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue SER 567 is missing expected H atoms. Skipping. Residue SER 568 is missing expected H atoms. Skipping. Residue VAL 569 is missing expected H atoms. Skipping. Residue LYS 573 is missing expected H atoms. Skipping. Residue MET 575 is missing expected H atoms. Skipping. Residue THR 582 is missing expected H atoms. Skipping. Residue MET 583 is missing expected H atoms. Skipping. Residue SER 586 is missing expected H atoms. Skipping. Residue VAL 587 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue LEU 589 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue SER 613 is missing expected H atoms. Skipping. Residue THR 614 is missing expected H atoms. Skipping. Residue LEU 615 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue THR 626 is missing expected H atoms. Skipping. Residue ALA 638 is missing expected H atoms. Skipping. Residue LYS 643 is missing expected H atoms. Skipping. Residue LYS 645 is missing expected H atoms. Skipping. Residue LEU 648 is missing expected H atoms. Skipping. Residue LEU 650 is missing expected H atoms. Skipping. Residue LEU 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue LYS 658 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue VAL 669 is missing expected H atoms. Skipping. Residue VAL 670 is missing expected H atoms. Skipping. Residue LEU 672 is missing expected H atoms. Skipping. Residue SER 673 is missing expected H atoms. Skipping. Residue THR 675 is missing expected H atoms. Skipping. Residue VAL 676 is missing expected H atoms. Skipping. Residue SER 679 is missing expected H atoms. Skipping. Residue LEU 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 685 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 690 is missing expected H atoms. Skipping. Residue THR 695 is missing expected H atoms. Skipping. Residue ALA 698 is missing expected H atoms. Skipping. Residue ILE 699 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue VAL 727 is missing expected H atoms. Skipping. Residue SER 728 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue LEU 751 is missing expected H atoms. Skipping. Residue ILE 754 is missing expected H atoms. Skipping. Residue LEU 764 is missing expected H atoms. Skipping. Residue THR 765 is missing expected H atoms. Skipping. Residue LEU 767 is missing expected H atoms. Skipping. Residue VAL 769 is missing expected H atoms. Skipping. Residue LYS 772 is missing expected H atoms. Skipping. Residue LEU 773 is missing expected H atoms. Skipping. Residue SER 775 is missing expected H atoms. Skipping. Residue LEU 776 is missing expected H atoms. Skipping. Residue SER 777 is missing expected H atoms. Skipping. Residue ALA 791 is missing expected H atoms. Skipping. Residue ALA 808 is missing expected H atoms. Skipping. Residue MET 810 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 830 is missing expected H atoms. Skipping. Residue LEU 832 is missing expected H atoms. Skipping. Residue ALA 833 is missing expected H atoms. Skipping. Residue ALA 834 is missing expected H atoms. Skipping. Residue THR 835 is missing expected H atoms. Skipping. Residue VAL 839 is missing expected H atoms. Skipping. Residue ALA 843 is missing expected H atoms. Skipping. Residue LEU 917 is missing expected H atoms. Skipping. Residue SER 919 is missing expected H atoms. Skipping. Residue TYR 920 is missing expected H atoms. Skipping. Residue LEU 929 is missing expected H atoms. Skipping. Residue ALA 962 is missing expected H atoms. Skipping. Residue THR 980 is missing expected H atoms. Skipping. Residue LYS 1009 is missing expected H atoms. Skipping. Residue LYS 1017 is missing expected H atoms. Skipping. Residue LYS 1020 is missing expected H atoms. Skipping. Residue THR 1035 is missing expected H atoms. Skipping. Residue VAL 1036 is missing expected H atoms. Skipping. Residue ILE 1050 is missing expected H atoms. Skipping. Residue SER 1082 is missing expected H atoms. Skipping. Residue SER 1087 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue THR 1101 is missing expected H atoms. Skipping. Residue LEU 1104 is missing expected H atoms. Skipping. Residue SER 1141 is missing expected H atoms. Skipping. Residue LYS 1143 is missing expected H atoms. Skipping. Residue MET 1166 is missing expected H atoms. Skipping. Residue LYS 1174 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue ALA 1199 is missing expected H atoms. Skipping. Residue LYS 1216 is missing expected H atoms. Skipping. Residue SER 1227 is missing expected H atoms. Skipping. Residue LYS 1253 is missing expected H atoms. Skipping. Residue SER 1257 is missing expected H atoms. Skipping. Residue SER 1287 is missing expected H atoms. Skipping. Residue LYS 1307 is missing expected H atoms. Skipping. Residue LYS 1318 is missing expected H atoms. Skipping. Residue LYS 1319 is missing expected H atoms. Skipping. Residue LYS 1329 is missing expected H atoms. Skipping. Residue ALA 1373 is missing expected H atoms. Skipping. Residue LYS 1390 is missing expected H atoms. Skipping. Residue MET 32 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 46 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue ILE 50 is missing expected H atoms. Skipping. Residue LYS 52 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue TYR 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 75 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue LYS 85 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue LEU 127 is missing expected H atoms. Skipping. Residue LEU 129 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue THR 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LYS 168 is missing expected H atoms. Skipping. Residue VAL 174 is missing expected H atoms. Skipping. Residue LEU 177 is missing expected H atoms. Skipping. Residue MET 180 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue LEU 186 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue LYS 197 is missing expected H atoms. Skipping. Residue MET 201 is missing expected H atoms. Skipping. Residue LEU 218 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LYS 245 is missing expected H atoms. Skipping. Residue LEU 263 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue ALA 306 is missing expected H atoms. Skipping. Residue THR 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue LYS 341 is missing expected H atoms. Skipping. Residue LYS 371 is missing expected H atoms. Skipping. Residue SER 373 is missing expected H atoms. Skipping. Residue ALA 374 is missing expected H atoms. Skipping. Residue VAL 380 is missing expected H atoms. Skipping. Residue SER 394 is missing expected H atoms. Skipping. Residue TYR 395 is missing expected H atoms. Skipping. Residue MET 415 is missing expected H atoms. Skipping. Residue LYS 422 is missing expected H atoms. Skipping. Residue LEU 423 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 434 is missing expected H atoms. Skipping. Residue ILE 438 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue VAL 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue THR 452 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue ALA 454 is missing expected H atoms. Skipping. Residue ALA 455 is missing expected H atoms. Skipping. Residue SER 456 is missing expected H atoms. Skipping. Residue ALA 472 is missing expected H atoms. Skipping. Residue LEU 476 is missing expected H atoms. Skipping. Residue SER 479 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue LEU 493 is missing expected H atoms. Skipping. Residue ILE 495 is missing expected H atoms. Skipping. Residue ALA 504 is missing expected H atoms. Skipping. Residue SER 512 is missing expected H atoms. Skipping. Residue MET 513 is missing expected H atoms. Skipping. Residue VAL 515 is missing expected H atoms. Skipping. Residue LEU 521 is missing expected H atoms. Skipping. Residue LEU 523 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue ALA 526 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ALA 534 is missing expected H atoms. Skipping. Residue ALA 537 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue ILE 551 is missing expected H atoms. Skipping. Residue LEU 552 is missing expected H atoms. Skipping. Residue ALA 584 is missing expected H atoms. Skipping. Residue LEU 587 is missing expected H atoms. Skipping. Residue LEU 593 is missing expected H atoms. Skipping. Residue SER 598 is missing expected H atoms. Skipping. Residue ALA 601 is missing expected H atoms. Skipping. Residue LEU 621 is missing expected H atoms. Skipping. Residue MET 626 is missing expected H atoms. Skipping. Residue LYS 634 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue LEU 643 is missing expected H atoms. Skipping. Residue LEU 644 is missing expected H atoms. Skipping. Residue LEU 647 is missing expected H atoms. Skipping. Residue LYS 648 is missing expected H atoms. Skipping. Residue LEU 649 is missing expected H atoms. Skipping. Residue ILE 653 is missing expected H atoms. Skipping. Residue MET 654 is missing expected H atoms. Skipping. Residue ILE 660 is missing expected H atoms. Skipping. Residue ALA 667 is missing expected H atoms. Skipping. Residue THR 683 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue MET 709 is missing expected H atoms. Skipping. Residue LYS 719 is missing expected H atoms. Skipping. Residue SER 720 is missing expected H atoms. Skipping. Residue LEU 722 is missing expected H atoms. Skipping. Residue LYS 729 is missing expected H atoms. Skipping. Residue VAL 739 is missing expected H atoms. Skipping. Residue LYS 742 is missing expected H atoms. Skipping. Residue LYS 763 is missing expected H atoms. Skipping. Residue LYS 769 is missing expected H atoms. Skipping. Residue LYS 784 is missing expected H atoms. Skipping. Residue SER 786 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue LEU 789 is missing expected H atoms. Skipping. Residue SER 807 is missing expected H atoms. Skipping. Residue ALA 820 is missing expected H atoms. Skipping. Residue ALA 826 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LEU 833 is missing expected H atoms. Skipping. Residue LEU 836 is missing expected H atoms. Skipping. Residue SER 839 is missing expected H atoms. Skipping. Residue ALA 846 is missing expected H atoms. Skipping. Residue MET 860 is missing expected H atoms. Skipping. Residue LYS 873 is missing expected H atoms. Skipping. Residue SER 891 is missing expected H atoms. Skipping. Residue ILE 892 is missing expected H atoms. Skipping. Residue SER 906 is missing expected H atoms. Skipping. Residue ILE 949 is missing expected H atoms. Skipping. Residue SER 972 is missing expected H atoms. Skipping. Residue LEU 1019 is missing expected H atoms. Skipping. Residue LEU 1022 is missing expected H atoms. Skipping. Residue SER 1070 is missing expected H atoms. Skipping. Residue ILE 1074 is missing expected H atoms. Skipping. Residue LYS 1078 is missing expected H atoms. Skipping. Residue THR 1107 is missing expected H atoms. Skipping. Residue THR 1124 is missing expected H atoms. Skipping. Residue LYS 1129 is missing expected H atoms. Skipping. Residue ALA 1180 is missing expected H atoms. Skipping. Residue VAL 1188 is missing expected H atoms. Skipping. Residue ILE 1217 is missing expected H atoms. Skipping. Residue SER 1219 is missing expected H atoms. Skipping. Residue SER 1221 is missing expected H atoms. Skipping. Residue SER 1223 is missing expected H atoms. Skipping. Residue LYS 1274 is missing expected H atoms. Skipping. Residue SER 1275 is missing expected H atoms. Skipping. Residue MET 1297 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8961 (mp) REVERT: B 170 ASP cc_start: 0.8732 (p0) cc_final: 0.8495 (p0) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.4106 time to fit residues: 50.6783 Evaluate side-chains 69 residues out of total 1990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1171 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 197 optimal weight: 0.1980 chunk 218 optimal weight: 0.8980 chunk 4 optimal weight: 40.0000 chunk 76 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 14 optimal weight: 0.0040 chunk 164 optimal weight: 9.9990 chunk 205 optimal weight: 0.7980 chunk 81 optimal weight: 0.0370 chunk 123 optimal weight: 8.9990 chunk 178 optimal weight: 20.0000 overall best weight: 0.3870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.084957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.059501 restraints weight = 187189.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.060415 restraints weight = 76709.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.060638 restraints weight = 43636.019| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15319 Z= 0.095 Angle : 0.438 6.407 20774 Z= 0.242 Chirality : 0.033 0.131 2369 Planarity : 0.003 0.052 2618 Dihedral : 13.986 179.751 2834 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 0.17 % Allowed : 9.59 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.68 (0.19), residues: 2151 helix: 3.45 (0.13), residues: 1624 sheet: None (None), residues: 0 loop : -1.09 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 679 HIS 0.004 0.001 HIS A1061 PHE 0.013 0.001 PHE B 933 TYR 0.008 0.001 TYR B 746 ARG 0.002 0.000 ARG A1068 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 1178) hydrogen bonds : angle 3.15413 ( 3465) covalent geometry : bond 0.00192 (15319) covalent geometry : angle 0.43829 (20774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7025.53 seconds wall clock time: 120 minutes 39.41 seconds (7239.41 seconds total)